You Form W4 impacts the amount of withholding that is going to be on the W2, so changing filing status at tax time might mean he may owe more taxes now if he fils MFS (because he claimed MFJ on his W4, less taxes would have been taken out on his paychecks than if claimed MFS).
However, your Form W4 has no impact on what you can or cannot due on your actual tax return. You still have the option to file either married jointly or separately, whichever results in the greatest tax savings (which is usually married filing jointly).
Are you considered MFS due to student loans because of income based repayment or because of being behind in payments?
You can look into filing Form 8379 for injured spouse to protect his share of the refund if you are concerned about filing jointly due to past due student loans.
https://turbotax.intuit.com/tax-tips/marriage/what-is-irs-form-8379-injured-spouse-allocation/L7tsrx...
