Well, I think the best reason why this isn't the case is cos I doubt Kishi would dissapoint (again) fans with Naruto's newest training, only to have him turned into a frog.
There are three types of people in the world. Those who can count, and those who can't.
also Naruto has a few things going for him in terms of fighting a genjutsu user... first off in senjutsu mode he will now have Fukusaku on his shoulder to dispel such a attack, second his chakra reserves are so high he can potentially dispel even a complex genjutsu on his own, and finaly with the 8 tails having escaped there seems to be a high possibility that Naruto at some point will learn to master the QB... meaning he will have the ability to be released from genjutsus such as the Tatsukumi with the help of his Tailed beast just as the 8 tails performed... but in terms of just senjutsu vs. genjutsu I think that its pretty obvious under the principles of how both arts work that senjutsu would have an understandable advantage over genjutsu.
"I hand out pockets full of ass whoopin to the poor" -Emperor Yatar
Cant you break out of Genjutsu if you increase your chakra and if that fails someone has to give you some of their chakra. If thats the case, then the only genjutsu that should hold Naruto in sage mode is Itachis MS technique (cant remember the name), but even with that Saskue broke out of it, so Nartuo should be able to as well.
I don't think after Naruto is in Sage Mode he will turn into a frog, actually I think he will be able to dispel even the strong genjutsu because the amount of Nature energy runing trough him, and if he is using clones to absorb chackra it will be even better I guess we will have to wait a bit to find out about it