The native Apple TV OS (both 1 and 2) can learn a new remote. But full Mac OS X cannot. If you have a learning remote, it can learn the Apple Remote commands and reproduce them.
But his problem was that the ATV1 reacted on the Apple remote when using it with ATV2, or did I get that wrong? So having the ATV2 learning the TV remote and not use the Apple remote would be a solution.