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.
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.
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.