
Quoting
Taxing Matters
Generally after 3 years the IRS cannot assess any additional tax nor can the taxpayer get a refund of any overpaid tax. But in some cases it can be worth amending a return filed more than 3 years ago so that the information is accurate even if any tax change that results cannot be collected/paid due to the statute of limitations. This might be one such circumstance if the mistake on the marriage status on the returns would affect the security clearance review and if the amendment might look better in that review. Not knowing exactly what security clearance is being sought, I cannot say if it would be helpful here. I simply wish to say here not to reject this possibility out-of-hand.
You need her signature if you wish to amend to a joint return; you don't need it to amend to married filing separately.