First, you needed to file married filing separately, not as single, so if you actually filed as single you will need to amend your return to show your acutal status as married filing separately.
For the issue of removing the conditions on your residency, joint tax returns are helpful as evidence of a bona fide relationship. However, filing separate tax returns is not going to get your removal petition denied so long as you have ample other proofs of a bona fide relationship. I would also enclose a letter explaining that the filing status was a purely financial decision.
When you are married there are only two choices for filing your tax return. Either married filing separately, or married filing jointly. Therefore, the tax return you filed as single when you were married is incorrect. The correction is made by filing an amended return (Form 1040X) and checking the correct filing status. This may cause you to owe more in taxes.
You should also correct your filing status on your Form W-4 with your employer so that they withhold the correct tax from your paycheck.