Bad argument, Itachi's genjutsu revolves around eye sight, dojutsu, and Ma + Pa's was sound genjutsu. Completely different. We don't know whether Dojutsu Genjutsu will work on the Rinnegan, as it is the superior Dojutsu, but, for your sanity, let's say it will work.
Itachi's genjutsu may be able to control his senses, but, they can still move in the real world, as seen when Itachi put Naruto in a genjutsu and he ran and Rasnegan'd thin air, as well as this, all Deva needs to do to cast Shinra Tensei is, some what widen his eyes, as seen vs Kakashi, and his genjutsu could not stop him doing this.
If he get's hit with Tsukuyomi, he will take considerable toll but as his life force is Nagato's, and Nagato is an Uzumaki, his life force is strong, so the effects of Tsuku will not be as drastic as with other people, this is not me saying it won't effect him, but he may tank it a lot better than others could.
Saying this he should still be able to Shinra tensei whilst in the genjutsu.
Despite all of this, Nagato knows Itachi is a master of genjutsu and will not allow himself to be put under as easily as you suggest.