I think, in fact, that it is healthy and natural for people to gang up on weaker or stronger opponents. As the Hitler-Stalin example illustrates, this is the sort of thing different religions, even if they completely hate one another by dogma, would do for their own self interest.
The problem I have, so far, is with non-agression pacts. Players of dom3 have read too much game theory, or are too honest, or whatever, and are TOO TRUSTWORTHY.
As yet, I have never had the terms of a NAP betrayed - I've had wars after a NAP expired, but even those are rare. I feel kinda silly complaining about this, but the fact that everyone keeps their word makes non-agression pacts too attractive.
Maybe I just haven't played MP with a diverse enough crowd - but in ferion, for example (
www.ferion.com), people trech (or bend the words of a non-binding treaty) all the time. Of course, ferion has built in, game mechanical, binding treaties - so these agreements are between alliances (i.e. alliance 1 and 2 agree to attack alliance 3 until it is dead, but alliance 2 attacks alliance 1 slightly before alliance 3 is finished off.)
To this end, I think game mechanical support for alliances, NAP etc. might almost be preferable, as players might then feel free to trech on non-binding gentleman's agreements etc. But this opens up an entire diplomatic can of worms that might ruin the (highly attractive) simplicity of dom3 politics, so I think it's probably more trouble than it's worth (coding difficulty aside.)
Anyhoo - if you have a gentleman's agreement to not communicate out of game, and if all in-game messages are suspended, that ought to be sufficient. You'll still get an occasional pre-arranged cheater, but approaching your neighbor and offering a NAP (if it is forbidden to do so) is probably enough of a risk that people wouldn't do it.