Officers were in majority Serbian (hard to give percentage). Historically Serbs tended to see army service as something honourable. Example: in the Army school initial intake was matching Yugoslav census but by the end of schooling many non-Serbs dropped out. Also other ethnic groups started leaving once political tensions rose. When mobilisation started JNA sent recruitment notices too all nationalities but mostly Serbs responded to it which only cemented Serbian majority. This led to a rise of Serbian Army. I don't remember any place where a complete unit (in game units) switched the sides.
I would have events to demoralise JNA units (e.g. Slovenian government recalls it's officers from JNA) to keep game going otherwise it's all done in a week.