Ha ha, you think FMF people don't want to kill each other? That's cute.

Seriously though, Iron Kingdoms is all about the "the enemy of my enemy is my friend" concept. Also, just because they eat what they kill, doesn't mean they kill everything. Granted, interactions between different races are probably pretty tense, and not very chummy, but it's not really any harder than having Khadorans and Cygnarans trying to work together.

An easy way to handle this is to give them all a common enemy that none of them can negotiate with at all. Cephalyx, Cryx, and Everblight are all really good examples of people who you'd need to work together with people you don't like in order to get rid of. Just because you're a troll who hates gators doesn't mean you won't get the gators to help defend your kriel from Cryx moving into the area.

Then let them work together to deal with a somewhat less extreme enemy, like Khadorans or Convergence cultists. Maybe they can work out a peaceful outcome, but probably not.

Now that they have been allies a while (even if it's not a friendly alliance), they have a certain level of trust and even dependency with each other, and basically anyone that isn't them can be seen as an "outsider" that warrants a cooperative approach to handling them. Another gator tribe is moving in and causing trouble among yours? Who better to call than your non-gator buddies who aren't influenced by your tribal politics to come and deal with them?

The key here is mutually beneficial arrangements. If you need something extreme to get them working together right off the bat, my personal favorite is starting the group off as prisoners. They don't have to like each other to understand that they need each other to survive/escape.

It's definitely trickier than some games, but really it just keeps you from ignoring some of the great character conflict that should be in all games. If someone's running an Eberron game with a Karnathi soldier and a Aundairian wizard without having to work up some reason why they aren't at each others throats, they're missing out on one of the things that make that world great.

Something I like to do (if I trust my players to be creative and not bumps on a friggen log), is run through the "Phase Trio" part of the Fate character creation process. If you aren't familiar with Fate, you basically have the players tell you why they work together. It adds a bit of time to character creation, but it can also be a fun part of the game.

Hopefully that helps. Best of luck to you.