I know that both my husband's MK experiences and the train wreck that is the QF/Patriarchal Christian home school community have BOTH caused me to rethink Christianity, and it's a very positive thing! I think the current Christian home school business model can make a home school a bad spiritual experience as well. It has the same continual demand for spiritual maturity and moral perfection on children that you MKs got in boarding school.
I was just apologizing to my daughter for attempting to take the place of the Holy Spirit in her young life, and for being pretty much constantly disappointed with her during her adolescence. Instead of accepting my daughter for who she was, and letting God lead her character over time, I had all those evening devotions and Charity Churchmouse videos, etc. constantly calling for moral perfection in children. I was quite frustrated with her where she didn't measure up.
Eventually, when we almost lost her to an abusive boyfriend, I said "Screw all this religious crap, I am just going to love on my daughter right where she is!" The day I took her to the doctor for birth control pills was the day our relationship began to mend. My actions told her that finally, who she was and what she was going through were more important to me than my religion.
That was three years ago. She calls or texts me everyday now, and drops by the house to hang out at least once a week, sometimes twice. She goes to church with me about once a month, out of love for me and because she loves worship and communion. I think she heard enough sermons by the time she was ten to equal probably fifty years of Sundays, so she's still ahead of the game there.