Any idea why the program is hanging? top shows the process using next to no CPU time and very little memory.

I'd suspect a locking problem; have you made sure that no other mail-related process is trying to access the mailbox while you're deleting the unwanted messages ?

You haven't said anything about what type of OS and/or Mailbox you have. If things are happening on Linux, you might see which processes concur to access the mailbox using fuser:

fuser -uv mailbox_filename