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.
Lord Emperor would catch a lightsaber with his teeth and spit blaster projectiles into Revan. Considering how many paradoxes Revan book has, I say, Lord Emperor would wipe all of them at once and then he would make a new cape for Lord Scourge