I would prefer it if they took out the honorifics. The characters sound weird and unnatural saying them. JUNPEI-COON! SENPAISENPAISENPAISENPAISENPAISENPAI!
A lot of JRPGs sound great, even without honorifics, so for a superb series like Persona, taking them out isn't going to cause any problems. Unless you're a hardcore japanophile who absolutely needs to be called senpai every 10 seconds. Just my opinion. I know many people will disagree with me.