OK I think I've been able to figure out why this pisses me off. There's going to be a bit of armchair psychology involved, so take this with a massive grain of salt, but here goes:
It's quite obvious that this sequence of events is in no way realistic for numerous reasons, but it's not the fact in itself that makes me hate this storyline. It's quite obvious that Willis has problems with his religious upbringing, and that the comic is semi-autobiographical. However, it's that semi part that is troubling. Basically, this whole plotline is one big revenge fantasy where he gets to defeat his evil religious family members and come out on top triumphant, which is why nobody gets hurt and everything is all hunky-dory at the end. This pisses off normal people because it makes light of real life tragedies, like school shootings, familial abuse, and so on, just so Willis can selfishly exploit his characters for his own personal benefit.