Can Gatekeeper be disabled via terminal in OS X 10.8 Mountain Lion?
The spctl tool should do the job.

sudo spctl --master-disable will turn off the Gatekeeper checks, and sudo spctl --master-enable will re-enable them (to the default setting of App Store and signed apps — it doesn't appear that setting it to App Store-only is possible).

Note that it will not throw any error if you run it without sudo permissions, but sudo is in fact required.