It's quite terrible. I even reported it on bugreport.apple.com on 10.8.0, but neither 10.8.1 nor 10.8.2 fixed it.
I can't believe there's no-one at Apple using i18n keyboard layouts and Terminal.app.
It's not like typing "~" is an uncommon event on the command line....
Meanwhile, VLC fixed the same bug (typing ~ in the VLC.app UI textfields) in about 30 minutes.