The use of phrase "per se" in academic writing
I guess my advice would be to write in the way that seems most natural to you and gets your ideas across efficiently rather than worrying about the "word police."

If a reviewer objects then you can make a change, or not, as you see fit. 

Clearly objectionable terms would be an exception, of course, but reviewers will point those out pretty regularly. 

I think it is a fair statement to say that language rules evolved from language usage and not the other way around.