I feel as if Meetra killing the Emperor via a lightsaber throw being a rather...anti climatic ending, I mean sure there have been worse deaths then that but...I mean I just dunno. Speaking of that, wouldn't killing the Emperor stopped his attack anyway thus saving Revan aswell and killing the Emperor? Just throwing that out there.
Well the way I see it, Meetra saw the Emperor about to kill Revan, who she had an emotional attachment to and saw it as her duty as a Jedi to protect. It such a way her purely instinctive action would be to deflect the blow. I doubt she even considered in that split second, throwing her lightsaber at the Emperor himself. So in a sense it wasn't a choice, just an instinctive action based on her subconscious persona.
Alternatively maybe she just didn't realise that the attack could have killed the Emperor, maybe she thought he would deflect/dodge it and then kill Revan.