Yes, this exemption applies in your case.
As you have noted, a nonresident alien who elects to file jointly with a U.S. spouse qualifies for an exemption from the penalty for not having health insurance.
Although Publication 519 says that a non-resident alien who files married filing jointly with a U.S. resident is treated for tax purposes as being a resident for the whole year, this does not affect your spouse's ability to claim exemption from the provisions of the Affordable Care Act.
Check here for a list of the exemptions
from the ACA and details about who qualifies.
