Yes, we have consensus that is the way we will do it.  I should probably turn https://gist.github.com/gavinandresen/2355445 into an informational BIP.

RE: malleability:

Orthogonal (but related) issue to IsStandard.

Detecting Scripts that leave extra items on the stack will be done in a different part of the code than the code addressed by this pull reques. No need to execute the Script twice to figure out if it leaves extra stuff, and the idea behind IsStandard is to get to a quick yes/no before running a potentially expensive Script execution.