Burke as an Enclave agent wouldn't make sense because of a simple fact: if they do take the time to detonate a nuke just to erase a small settlement like Megaton, which isn't exactly powerful, while doing nothing to destroy Tenpenny Tower, which have a better organized (and armed) security force. A bit pointless. A little bit too pointless, if we consider that: a) they get nothing of it that helps their bigger plan and b) that within their bigger plan, killing both settlement's population is implied without an extra effort. Remember, they'd rather get killed by drinking water, why bother?