I don't mean to offend here, but as I said, I don't think the musical was written to criticise the Church of Jesus Christ of Latter-day Saints with any degree of sincerity, that is, I think it's pretty light-hearted.
While I understand that some people would be offended, I think the musical actually, as you've said, did create some genuine interest in the Church, and surely that's a good thing no matter how it came about?
I did honestly enjoy it, and I think everyone who has seen it realises that LDS isn't actually like that, just like not all orphanages are like the one in 'Annie'. It's a satirical production, it's common sense to assume that it's been exaggerated for entertainment value.
It's a genuinely uplifting musical about friendship, and how much good religion can actually do.