PBA asked, “Is an apikores really allowed to duchen? Anyone know?”
Rav Ovadia Yosef says that a Mechallel Shabbat should not duchen. I don’t remember about a apikoros, but I would infer that’s worse; i.e. don’t let him go up. In any event, he says that we allow the mechallel Shabbat to go up bediavad with frum Kohanim to avoid machloket. IIRC it all you got is a mechallel shabbat, then no Birkat Kohanim.