In the episodes Dark Water and Death in Heaven, was the intent in any way to mock Christian beliefs?

No. I don't think that was their intent.
And the Cybermen weren't necessarily rising from the dead, being they were never dead. The water made it so only organic material was visible, hence why we could only see skeletons. Their armor plating isn't organic. The skeleton, however, is. The Cybermen were alive the whole time; they were just being hidden from the public until their use became necessary.

But again, no, I don't think the BBC intended the finale to be a mock towards Christian beliefs.

They did not make it to mock Christian beliefs.