It would be nice if a future season presents somebody of faith who is a good guy though.
Well that's the thing--from what I've read, not even the second season does that. And if you read up on some of Warren Ellis' views, it's kind of hard to imagine there's not a bias there. In any case, it's not just the fact that this is yet another "big, bad anti-science religion" portrayal in an entertainment property--although I am sick to death of that--it's that that view Ellis presents of the Church's role in the world of scientific inquiry is actually kind of dated and based on poor research. There have been volumes of books written on how the Catholic Church built universities and promoted scientific inquiry, not halted it.
Were there religious figures who characterized advances in medicine as witchcraft? Undoubtedly. Do such figures belong in the place and time period in which Castlevania is set? Furthermore, do they even belong in the story of Castlevania III? I don't think so.