I was thinking of Jane Doe too, but I still have my doubts, since we don't know why Kyon called himself John Smith in the first place. It'd be kind of annoying if it turned out that there was a good (and important to the plot) reason for it, and the choice of Kyonko's alias wouldn't match it at all...
Then again, that applies to whatever name is chosen, so... Kind of a dead end here
