To be fair, the only person we've heard talk about Mohammad was Isaac, a Muslim who murders people to make them into living hellspawn to use to murder other people. Who gets pissy at 10 guys at the docks who don't want to let him and his army from hell into town, and decided that since they don't want bloodthirsty monsters in their town, that they are there to protect, clearly Isaac is doing the right thing by killing every man, woman, and child in that town.

No offense, dude, but if Osama Bin Laden is your only source on the Wisdom of Mohammad, you're gonna get the same insistence on his wisdom that you do from Isaac. It's the blind foolishness of the mad zealot.

Meanwhile, no condemnation of Christianity has been made. Plenty of condemnation of certain clerics and the same blind foolishness of the ones who listen to them (the townspeople who assented to the death of Lisa Tepes in season one, despite her having been their doctor and they knowing she was no witch or evildoer,) but Sypha had nothing but complements for Christ and His sacrifice.

Now, I'm no apologist for Warren Ellis, the man can eat a huge sack of dicks and his "climax" (pun intended) to many of the storylines in Season 3 were asspull bullshit that didn't follow one character's motivations, didn't explain another character's purpose, was obviously coming from a MILE away from episode one... But if there's any condemnation in Castlevania, it's not for any specific ideology, but rather for anyone who doesn't fucking act rationally, which just happens to be pretty much every single human being.

But honestly, so much of that is just the base storyline behind the games, so I don't know how much Ellis' asspull cucketry will ruin it going forward.