I suppose Father Jessup might count then.
I think Father Noel Furlong was just extremely annoying and possibly insane, as opposed to outright villainous.
I guess there is the Nazi priest, I did considered him, but he wasn't really that openly villainous despite his ideology.
I don't think Richard Wilson should count, sure he did beat them up, but he didn't seem villainous, just really sick of people bothering him with that catchphrase while he was trying to enjoy his holiday.
Eoin McColfer, now I don't remember them, remind me which episode were they in?
And oh yeah Sister Assumpta deffinatly counts, she was insane, abusive and sadistic. How could I forget her? That was one of my favourite episodes.
I look forward to it, if you want some help I'll be happy to create a couple.