No, Itachi is protecting Sasuke because that his little brother it clearly states he loved Sasuke more than his village.
Itachi brothely loves his brother, Sasuke. :'''')) <3
Isn't he suppose to be in a genjutsu with a command line to "Protect Konoha"??
He received information that Sasuke is trying to strike against Konoha... so I think Itachi has to consider Sasuke an enemy.
Itachi is under the Kotoamatsukami, for god sake.... at this point doesn't matter who is the person that is gonna attack the Village.
That command line "Protect Konoha" is the priority!!