If Naruto's only lending chakra and Naruto would transform it into something counter effective the Sharingan would be futile in controlling it.
???

Naruto's lending chakra?

When Naruto's under Genjutsu control, his chakra's being manipulated. He can try to snap out of it himself, or otherwise have an external source insert a surge of chakra into him to disrupt the flow of the genjutsu caster.

Since he has the Kyuubi in him, I thought that it might have worked as the secondary source.

But if the Kyuubi can be controlled by the sharingan, then when Naruto is under genjutsu the Kyuubi itself may also be affected, thereby stopping it from being able to make a decision to forcefully insert chakra into Naruto.