Easy: Summon a crow, pluck out one of its eyes, restrain it via genjutsu so it won't attempt to scratch your pretty face, shove your best friend's Mangekyou Sharingan into its empty eye socket, de-summon it.
I would think that a genjutsu would have been placed before Itachi took out the crow's eye in the first place. I dunno about you, but I wouldn't just sit there while some guy with black hair tried to take out one of my various tools for survival.
But that would make sense, I guess. The crow must have either had larger than average crow eyes or the socket was "adjusted" to fit the eye in there. Or it was a larger than usual crow with an eye socket big enough to fit it in there.
Either way, that crow probably would never be the same after the incident.