I honestly see this as a huge possibility. Sasuke's wanted to kill him since he phased through him back before the Bee fight. Sasuke could totally do this, again separating himself from Naruto.
It'll give Naruto and Sasuke even more reason to fight. Naruto obviously can't have Obito at large but after being in his head and seeing everything they have in common, he'd be PISSED if Sasuke murdered him instead of Konoha deciding his judgement.
It gives Naruto and Sasuke more tension and shows the difference in their way of doing things, that being how Sasuke would deal with this situation as Hokage, much like the bijuu.