My wife and I live and work in different states for the whole year of 2008 (TX and NJ respectively). What would be the filing status for us?

Turbotax suggested Married Filing Jointly but when it does the state tax (NJ only because TX has no income tax), it also counts my wife's income (not from NJ at all) and we will end up paying a lot more than filing separately?

If we file Married Filing Separately, does my wife still need to file an NJ return ($0 because no NJ income)?

If you are filing joint federal return, then you should file joint return for NJ. Your wife is nonresident of NJ and has no NJ income.
Read: Your U.S. Tax Return: Working or Living in Two or More states