It's not that they aren't available, it's just that they're ineffective. The aliens don't all have the same physiology, so you can't use an allround tranquilizer on them all. Plus, we already decided we would not include a toxigun equivalent into the game. Rubber bullets wouldn't be effective at all against most aliens (though they might work against human enemies), and pepper sprays aren't military weapons in the first place. It would be silly for PHALANX to even issue them to soldiers.
An electrolaser is in the works, however, and it may have stun capability.