I want to be very careful here, because
a. I was an offender on this and
b. I want to make it abundantly clearly that I'm going to follow community's and moderator's lead on this.
That said, I am afraid the "all questions sparked from comments belong on meta" solution may end up doing more damage than the problem it is trying to solve.
I, personally, like the comment traffic (although I agree, it should be moved to chat, and I intend to start doing that). I like being challenged on the assertions I've made, and many times those assertions lead me back to real questions about Christianity as a result.
In my offending question on humanism, I actively wanted to understand what differentiates a Christian from a humanist, if that was the definition. Marc Gravell made some really good points, Jon Ericson made some really good points, and the discussion really tied back to what Christianity is. That was actually sparked from a chat conversation, but I thought it uncovered a really question - Is Christianity just being nice to people? If so, what differentiates it from humanism? In hashing out these answers, both Jon and Marc brought really good sources to bear on the question.
In the end, I think that "bad question" (which earned a "Nice Question" badge) fostered information exchange in a good way. If our goal is to foster information exchange, it succeeded!
I realize we are not a discussion board - but I think there is also a qualitative difference between Stack Overflow and Christianity.SE.
Stack Overflow is meant to be an information clearing house. Get in, get out, get your solution. Christianity has very few "quick fix" type questions. People are bringing questions that have haunted them for years - and this site helps. People also are having their lifelong assumptions challenged - and this site helps do that. But in both cases, a 50 cent answer to a million dollar question should always raise more questions.
Those questions will in turn generate more questions, and should.
Christianity.SE is all about uncovering the unchallenged assumptions we all make. And, these all relate.
I'm afraid that a blanket rule of "move to meta from any comment" will just fragment the site into the juicy bits being on meta, and frankly a shriveling away of the main site.
When we are arguing what is and what isn't appropriate for this site, then clearly it should be on meta. But, if there is a serious attempt to understand implications of Christian doctrine and to challenge assumptions in questions, I do believe it belongs on main.
Indeed, I think its really good when a broad question is asked, an assumption is uncovered, and the assumption goes on to be asked.
That's good theology.
Again - I'm not trying to be a rebel, I just don't want to throw the baby out with the bath water.