Yes, you can file jointly with her. As a resident yourself, you can treat her as a resident by making an election. You would just need to add a statement along with your Form 1040. See Nonresident to resident
Yes, you can apply ITIN when she is not in the US. As long as you have all her original certified required documents.
Generally, filing jointly allows you to claim more benefits than filing separately.
For tax purposes, filing jointly with your spouse does not violate any regulations.
If you are treating her as a resident, you are required to report her worldwide income including any earned and unearned income like wages, interest, rental income.
