If you don't file jointly with your new wife, you must file as married filing separately (MFS). This is the only status you are eligible for if she chooses not to file married filing jointly (MFJ) with you. She also, has the same filing status options that you have.
It's important to note you must enter her social security number on your tax return and the two returns will connect at the IRS.
It may be the best advice to explain it to her parents because the issue will have to be addressed and you don't want underpayment or penalties later.
Regardless, if your wife's dad does file a return for her with a single status, you should file an amended return for her with MFS status. And you, yourself have no option but to file MFS or MFJ.
[Edited: 01.24.2018 | 3:31 PM]