http://matrix.org/docs/spec/#m-room-redaction is the current API for removing messages.
Matrix uses namespaces for extension to survive mutual parties extending it (http://matrix.org/docs/spec/#events), and we haven't seen any problems there yet.
That said, Matrix is still beta and we certainly do have a whole bunch of other problems :)
Oh, and I'm eager to see how their API survives mutual parties extending it. (There is a reason why namespaces exists)