The only time that MFS makes sense in your case is if she has the low income and very high itemized deductions. For example, if she made 30k but had 20k in medical expenses. The only portion of medical expenses that are deductible are those that exceed 10% of income, so she only loses out on 3k of the expenses, whereas filing jointly with your high income, y'all might lose out on much more.
The HSA and 401(k) contributions are above-the-line adjustments, not below-the-line deductions, so your high income does not reduce them. You can still try the return both ways as some have suggested, but you'll be better off MFJ with the facts presented.