Blaming the League would be too obvious and the League never had a reason to go kill Sara. Nyssa wouldn't of allowed it and I am pretty sure Ra's would of given grace due to Nyssa. What we DO know is that MALCOLM is a wanted man that Ra's DIRECTLY want to have killed due to the events that happened in season one without HIS blessing on it. If it had been someone from the League, Sara would of automatically been on her guard too, but she seemed like she wasn't on the run, nor felt threaten by the individual right before she got killed. It was someone she do not deem as a threat, and she acted bewildered as to why that person was even there to begin with. So it is SOMEONE that even SHE least expected it. It couldn't of been Meryln because the only person that knows he's still alive, aside from Ra's, is THEA. So, it has to be Thea.
As for a motive? Merlyn probably want the blame shift at LoA, considering they're out on the hunt for him. Thea is still sore from all the lies and deceit from virtually EVERYONE and basically broke bad and seeking a little payback.