Change iTerm2 Default profile preset with "defaults write..."
To expand on the existing answer, if you load the colours you'd like once then you can export your preferences list file from the 'General' tab to a location in your dotfiles.

Thus, in my setup script, I have:

defaults write com.googlecode.iterm2 "PrefsCustomFolder" -string "/Users/ojf/dotfiles/iterm"
defaults write com.googlecode.iterm2 "LoadPrefsFromCustomFolder" -bool true


As long as your custom folder plist also says to load from the same custom folder (!) you'll be fine.