Did you forget that Itachi is(was) under a genjutsu called Kotoamatsukami?
His ''orders'' set by Kotoamatsukami were: 'Protect the Leaf!'

But!
Itachi doesn't kill Sasuke (who is a threat to the Leaf), doesn't that make Kotoamatsukami a failing jutsu?
Since no one can resist Kotoamatsukami's order, Itachi had to disable Sasuke too in order to protect the Leaf, but he'll probably end up transferring some of his powers to Sasuke....powers which would help him destroy Leaf.

Sasuke is a member of the leaf, at least he is according to Naruto, so he can't just kill him.


Remember, Itachi said that Sasuke has another brother, Naruto.