Nah, that's not shade at John Paul II, everyone loved the guy, in Poland or outside of it. Hell, I am not a Christian, let alone Catholic, and still respect him.Well, after the shade thrown at John Paul II in TW3, I certainly wouldn't put that past them.
The Church of the Eternal Fire is problematic in the books for its racism against non-humans, and that is reflected with Hemmelfart, but the slight resemblance is really not enough to assume all that is directed at him.