The crow probably reacts to when someone tries to use MS Naruto, since it was originally intended to be a weapon of some sort against Sasuke, but since Sasuke has EMS now, I don't think it will work. Maybe it seals away doujutsu powers, so it'll seal away Itachis sharingan completely.
We haven't seen Sasuke activate MS against Naruto, everytime Sasuke has MS, Naruto aint there, like Sasuke vs Kakashi, Naruto appeared shortly after Sasukes MS deactivated.
Itachi asked Naruto what he would do if Sasuke was to attack Konoha, Naruto said he'll save Sasuke AND he'll save Konoha, thats when Itachi gave him the Crow. Probably for Naruto to be able to stop Sasuke without killing him, in other words, sealing away his sharingan.
It doesn't react to Kakashi's MS because it is never aimed at Naruto

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And I think its one-time only use. It's seal away Itachis doujutsu and Naruto will face against Sasuke with EMS without interruptions.