@Blueclouds my two cents ( and if I assume that your wife will eventually come back to USA and work either at the same entity or a different on), would be to let the accounting firm do the her Indian filing ( as only she would have Indian tax liability, and you do the US return covering MFJ. I say this because when she comes back you will have to pick-up from what the accountant have done for her US filing ( She as a US person is taxed on her world income for the calendar year by the USA and Distinct from her Indian taxes. I fully understand that this will be hard on you now but is better prepared for later.
The other option is you file as MFS, do your own taxes ( not that your state taxes may get a bit confusing if you live in a community property state like CA ). Then when her filings are completed, you do a dummy prepare it again on your own for the wife -- this way you will be familiar with what was done by the accountants. Will make the future transition easier.
If you have time you could try it both ways and see which is more tax beneficial -- doing it as joint will raise your tax bill a bit ( higher marginal tax rate possibly ) but doing MFS will reduce your own deduction. I say this because depending your individual world incomes it may or may not make a huge difference.
I hope this helps.
Namaste ji
pk
