Agreed... I don't really get this behavior. It's become extremely* common, especially here on Meta, and the reasoning doesn't hold up. I could understand quick deletion in the case of spam, or illegal content... But most of the comments I see removed are pretty benign.
The mass-deletion of extensive discussion might make some sense on SOFU, but given that Meta was created in part to provide a place to discuss matters pertaining to SOFU, it hardly seems appropriate to squelch those very discussions.
The system was set up to remove comments (and questions, and answers) that had been flagged n times, for some value of n. If that's not happening fast enough, then perhaps n needs to be reduced; otherwise, it should be left up to the readers to decide what is appropriate (again, excluding things that would create a liability for the site itself such as spam and content that breaks US law).
*Ok, so that's an extreme exaggeration - somewhere over 3% of comments on Meta are force-deleted. Perhaps I've just been more observant lately... Still annoying when it happens, but at these levels probably not worth a complete ban on deletion. It would be nice though, when a conversation is still "warm", if moderators would ease up on the big red button - it may not seem likely that any of us actually have jobs that distract us from continually refreshing the page, but it is frustrating to return and find a dozen or so comments gone without a trace or explanation.