However TM is being kept out of the app store for other reasons, such as it's ability to prompt for an administrator password to allow writing to protected files.
Apparently, you can alt-click and select open, but my gut tells me that this was an oversight and will not last long. This feature was touted as a potential way to protect children, and if overriding it doesn't even require entering a password it fails at that pretty badly.
http://www.apple.com/osx/whats-new/features.html#gatekeeper
And even explicitly mentioned in a system dialogue:
http://cdn.arstechnica.net/wp-content/uploads/2012/07/gateke...
I am still not on Mountain Lion, so I don't know if you need to enter a password (which children shouldn't have) or right clicking is enough?
xattr -d com.apple.quarantine myTrojan.app
Now you can run the application no matter what the Gatekeeper setting is set to. No need to be paranoid. Gatekeeper isn't meant to lock down the Mac against yourself. It is a security feature only.
You only need to change settings (or right-click and hit Open) if you are running unsigned binaries.