My wife and are both working in Eastern Europe as contractors to a U.S. Company. I have dealt with the exclusion before so I know that I will qualify for it. My question however, is this. My wife was not employed to work outside the U.S. With me at the time we arrived. She was later hired as an admin assistant. If she was not employed for the full 330 days to qualify for the exclusion but I am... how do we file? Do we file married filing separate or married filing jointly? Married filing separate will end up in a bigger tax liability will it not? What would be the best way to file in this situation and can we exclude any of her foreign earned income?

The physical presence test is based on the days you were abroad, not on the days you actually worked. So if you both pass the physical presence test you are both eligible for the foreign income exclusion.
Anyway, you can file a joint return and you could even if only one person would be eligible for the exclusion.

I agree with what TaxForAliens says, but you need to model the return BOTH ways to determine which way results in the least amount of tax.

If you want my professional help, double-click on my title above and scroll down to my profile/signature. You will find my email address and websites there.