You can file your federal return as married-joint, which will probably be better for you as far as your federal taxes are concerned. You will have to file as married-separate on your state returns, however, since your resident status is different.
The only way to do this in TurboTax is to file as married joint on one program to generate your federal return, then prepare two more federal returns to generate your separate state returns.
You can do this more easily in the desktop version of TurboTax, since you can file multiple returns using one program, as opposed to needing to set up and pay for three different returns in the desktop version of TurboTax.
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