I pronounce bona fide two ways. I don't know if it is right or wrong. I don't care because everyone knows what I mean and people who know me know that my answer to their correction will be that I know but I like to say it the way that I do.
If something is bona fide, I say it like it's spelled. BONE-a-fEYED.
If someone is showing their bona fides, I pronounce it in Latin.
I have more occasions to say bona fide like the former rather than the latter.
I don't know what the correct pronunciation usage is, nor do I care. My rule has served me well in my life thus far.