I am on many developers' mailing lists, and keep all my email around, sorted by the various dealings I have and subjects I have conversations on. The size and scope of some of my Mail.app folders causes it to try to re-index them just about every time I launch the program, which results in forced reboots as you've described. So I automatically open the activity viewer (Opt-Command-V) on startup and kill any indexing threads, and immediately rebuild the index from the Mailbox menu. This avoids most issues with locking up the machine.

I also quit the application when I don't want to be bothered by it, since after long periods of running time, just about any major operation (selecting another mailbox) will nearly instantly kill the machine. I'm surprised it took so long for this problem to be noticed by someone else, though I never considered the problem with scanning my remote shell account's home directory.