I can't find anything to suggest otherwise; it is perfectly valid (if somewhat slow) on NRE, while the Routeing Guide suggests that Stansted Airport is actually on the West Anglia Main Line and not on a branch! I've done Cambridge to Stansted Airport via Stansted Mountfichet before now, so I don't see why using the Airport station as a diversion would be a problem either.
But do note that the Stansted Express isn't really worth it; the FCC route is both faster and nicer, and has better trains on it (in my opinion anyway). You're too early to sample a 379 on the route as well, so that benefit doesn't apply.