On the federal tax return, a married couple can always file jointly as long as they both agree to do so, whether they live apart for job, military service, incarceration, marital unhappiness, or any other reason. As you found out, separate filing wipes out several important tax benefits. If you already filed separately, you can amend to a joint return. You would amend one of the separate returns as joint and mail it in. When it is processed, it will automatically cancel both separate returns. However, amending a separate to a joint return requires some manual adjustments that can only be done using Turbotax installed on your own computer, not online.
However, file joint federal return usually means you also have to file joint state returns, and this could subject your income to PA tax and his income to VA tax. There are some offsets involved, and your combined state tax should not end up higher than single state tax in the highest tax state. Assuming VA has higher taxes than PA (just a guess) then you would probably not be hurt by filing joint but your husband might owe more state tax than the benefit he would get back on federal.
This is a complicated situation and you may want to review it with a tax professional. There are limited situations where you can file joint federal and separate state, I can't even begin to figure out how those rules will apply to you without doing a lot of research (in states where I don't live!)
In turbotax, I would start by creating a new online account using Turbotax Deluxe to calculate and prepare a joint federal return with two states, and see how the numbers look (you can start for free--don't pay to file at the end because you can't file this return.)
If joint filing looks good, the next step would be to purchase a copy of Turbotax installed on your own computer, or see if you can get one for free from customer support depending on how much you paid to file your original separate return. In the end you could end up needing to prepare several different returns (amended federal, amended states with joint, amended states with separate, etc.) Start by trying the joint federal/joint state and see what happens.
