[gnachman]

Terminal does the same (for me). It's because opt-clicking above the line sends some up arrow keystrokes, which the shell interprets as moving back in history. In iTerm2 nightly builds (which are less stable than the betas) you can disable opt-click to move the cursor in prefs>profiles>pointer.

What's more interesting is the possibility of using the new shell integration features (https://code.google.com/p/iterm2/wiki/ShellIntegration) to turn off this feature just at the shell prompt. I'll open a feature request for that :)