If one of your allies attacks another ally, you remain neutral in the conflict, and both alliances are preserved. I've used this several times to remove pesky allies from minable resources that I could put to better use 
also: If a powerful enemy has powerful allies, I suppose that honoring an alliance could be the only way to fight the powerful enemy without also having to fight his allies at the same time. When you honor an alliance isn't it just against a single race, and not it's allies?
Quite the opposite. Wars between two alliances will almost invariably involve everyone on the map. When you join in a war to defend an ally, the game considers that the same as if you'd declared war on the people who attacked your ally; all their friends pile on you for attacking their ally. Be careful of the Altarians, they're almost as dangerous as a full alliance due to their super ability.
If you absolutely MUST attack a pack of allies, the best thing to do is to break your own alliances first. Then use the transport parking trick to get one of the allies to declare war on you. Use this to pick them off one at a time, rather than having your alliance members start the chain reaction that brings everyone on both sides into the war.