You named two suggestions, either: (1) better clarify the rule, or (2) adjust the rule so that it simply bans joint-frequencies with allies and nothing else. I'm going to explain why this current rule NEEDS to stay and potentially need evolved over time and why I agree with your first suggestion over your second. The following points I'm about to make is generalised based on the past several months and isn't intentioned to point any fingers at any specific faction.
THE NEW RULE
The rule is still fairly new and people are still navigating the different nuances and contexts of it. Like every new rule that gets introduced, we cannot expect it to be perfect at first. On top of that, it is also having to ensure that every member of your faction is clued up in understanding the rule. The back-up/joint frequency rule is one of those rules that can be broken easily if not understood. All it takes is one person to be rolling with another gang while still staying on the same frequency, and then out of nowhere requesting for back-up. Of course, their members are going to respond without knowing the context, because how could they not? Their member's life is at risk. However, at that simple request alone, this becomes outnumbered 2:1 and the outcome of the RP scenario has been changed to the point that it can't simply be OOC resolved. The forums should not solely be a place for punishment, but also to help staff clarify the new rule. If one faction's understanding of the new rule is different to another, then there are going to be situations in-game where one faction will think the other one is breaching it. This is unavoidable. It is also extremely difficult to understand the absolute source of where that back-up has come from without checking logs or reviewing evidence closely, sometimes. It is simply a learning process and a way for all gangs to eventually be on the same page. Should the new rule be written? Yes, I think so eventually. But at the moment, it is too contextual and just needs more time to evolve.
The rule is simply as it stands; If you did not come across the situation organically, then you cannot assist. You either have two options; (1) assist on your own or (2) leave and spare your character's life.
So I agree, this rule seems really good on paper - and it has been VERY good, honestly - but it just needs reworked and can only be reworked over time as more context is placed.
RP DEPRIVATION
As someone who was on the other end of the massive gang alliance (apologies that I don't know the exact number of factions involved, I just know that we were severely outnumbered), my motivation RP, as well as others', depleted completely. Any potential ideas, storylines, diplomacy meetings with other gangs, and RP scenarios had to be at a standstill/pause because we were expected to fight every day and for multiple times a day, often with very little escalation. At times, we had plans for RP, but it was constantly delayed because of a recent fight/upcoming fight/people were no longer motivated to carry out the RP. This deprived my faction of RP as well as our faction leaders' motivation to plan any for our members, which in turn deprived RP from factions that we wished to RP with.
If anything, I think the health of the server has improved significantly since the introduction of the rule. My faction was finally able to focus on building relations outside of fighting as well as focus on our own backstory/lore/turfs. It's also helped our members bond with one another internally since we only have one faction to focus on and that is ourselves.
LIMITATION
What I've noticed during my time on the server is when you give someone an inch, they'll go a mile. When you give people drug tables to place at home, they'll stack it on top of each other. When an OP bike is available on the server, people will buy it for millions. When a job is buffed, then people will do it all day, every day. Not to say that I wouldn't do the same, because why wouldn't I? However, when you apply this to alliances - when you don't limit them - then people will group in obscene numbers with no other motivation than to fight and provide back-up. This is why the rule needs to stay because without it, then everything I mentioned under RP deprivation happens, and if that continues, then people will be so demotivated that they will be pushed out of the server completely.
SMALLER GANGS
To continue from my previous point, I feel like the server is at a place where small gangs actually have room to grow. Yes, smaller gangs can no longer ask for protection from bigger gangs, but why should they? Small gangs need to prove that they can fight on their own without the help of others. If say two smaller gangs are fighting one another, and one small gang has the advantage to request help from a bigger gang, then wouldn't that demotivate the small gang that they were fighting? Wouldn't it be better for the two gangs to sort things out between themselves and therefore eventually meet to discuss diplomacy?
ALLIES THAT MAKE SENSE
I think it's important for every faction leader to really sit down and consider what their true intentions are with their allies/back-up. If your ally-ship only extends as far as having a "shared enemy" and to fight, then they need to question whether or not you are truly here to RP. For example, Daichead Gadai would never ally with a British faction because of their backstory pertaining to the IRA. Being any more than friendly with a British faction would be in COMPLETE opposition to our lore and purpose of the faction. Instead, we have created close relations with Chinese factions (due to shared colonialism from the UK). At an OOC level, we also nowadays also only advance relations with factions that we believe are on the server to RP.
At the end of the day, as I always say, it always comes down to the responsibility of the faction leaders. If you're a faction leader that wants to measure their faction's power by number of fights won, then of COURSE no longer having an active joint-frequency or back-up to call is a nerf to criminal RP. You will actually find that fighting together really only accounts for 10% of building relations.
If you really, really, want to build relations and group up... then what's stopping you? A joint-frequency or inability to back-up a gang should not stop you from RPing with another faction. Is the rule stopping you because you want to hang-out to eventually fight?
There are other ways to build relations, you just have to be creative. Some ideas (but not limited to) include needing help to kidnap someone specific to torture them, assisting another gang to help run their business, heists, bank-robberies, requesting help for illegal car modifications, food drives through Little Seoul, inviting HC to a planned private dinner, requesting for help in picking up a non-script shipment, requesting urgent (non-script) medical first aid from an ex-medic from another gang as a result of illegal activity, randomly showing up and turfs to gift blunts to a specific group of people, or just passively through community events/meet-ups. There are many things you can do.
TL;DR - +1/-1 The new rule is great and needs to stay, just needs more written clarification. New rule has helped RP excel in ways beyond simply fighting. Out of everyone, faction leaders should be pinned most responsible. RP should not be limited to just PVP and building relations through helping other gangs PVP. There is more to the server than that.