Yep. It's really the only problem I've got with the Jovians - not that they're not flawless people, but rather that really the only example of Christianity in any form still existing has them as Warhammer-esq Catholic Space Nazis. For Reasons.I've come to the conclusion that the Eclipse Phase writers don't really get religion, on a fundamental level.
Actually the Jovians themselves are fine. Not flawless, but you can't say that about any group of transhumanity, and they're better than some. Plenty of interesting ways to work with them in game, plenty of good plot hooks.