It was actually Tsukuyomi first and then Ammy or Susanoo, but your argument makes sense. I was wondering earlier how Itachi was activating the crow if he was under Kabuto's control, and if it was really going to be the same case it was with Hanzo when he broke free and stabbed himself. However, if it was really a counter against the sharingan, it'd be weird for Itachi to say "Let's see what happens." It's easy to say that Itachi simply didn't know how it would fare since he never used it before, but I find it hard to believe that the perfect Itachi would be portrayed as someone who was uncertain of his own techniques.
- In the current chapter, Itachi's right eye activated, so it looked like he was about to use Amaterasu on Bee. Itachi's left eye then activated at the last second when Naruto tried to warn Bee, so he is either using Tsukiyomi in response to Naruto interfering, or possibly using Susanoo (because both eyes were activated at the same time).
- I believe that the mind control wouldn't allow Itachi to willingly cast a jutsu to help his opponent, so I don't think it's possible he was activating the crow himself, I'm pretty sure that the crow was activating automatically in response to Itachi's Tsukiyomi (or possibly Susanoo)