score:7
Yes, she can apply for a visa as a family member of an EU citizen. It doesn't matter how she got her ILR/residence permit/etc, that's irrelevant for the Schengen visa rules. She is the spouse of an EU citizen, so she's eligible to apply on that basis.
As she is eligible to apply as a family member of an EU citizen, she should do so - the application process for family members of EU citizens is accelerated and free of charge.