YMM

I think the references to Jesus are real, but aren't there to simply tell the story of Jesus.

Maynard is describing loving someone who hurts you (though not on purpose), even before the biblical allusions. The bible comparisons just strengthen this meaning by comparing it to how Jesus loved humanity and was crucified.

Or, the lyrics could not be referring to Jesus at all, and he is just referring to Jesus in the title to say that his mother's relationship with Jesus did nothing but harm her (as at this time it would appear he was still angry about that).