First, a note about filing extensions for the state returns. If the Georgia return is showing a balance due, then that balance due is expected to be paid at the time you file an extension. The extension is for extra time to file, not extra time to pay.
So, you have to weigh the option of whether to go ahead and file the returns as is and then amend both returns if the employer comes through with the corrected W-2 or whether it is best to file extensions. Filing the Federal return now should be fine without an extension since the issues are with the state information on the W-2.
If the W-2 is truly incorrect in the allocation of income between the two states, meaning that he did not actually perform work in Alabama for 97% of the year, then filing extensions and waiting for the corrected W-2 is probably your best course of action.
If you know what the W-2 should be reporting, you can certainly type in the 'correct' values in TurboTax now before filing the returns so that you can see what the outcome should be. Just be sure to change things back to the actual W-2 values before filing any returns or extensions.
**Say "Thanks" by clicking the thumb icon in a post
**Mark the post that answers your question by clicking on "Mark as Best Answer"
