Since his chakra is not balanced perfectly, then he would have to have less natural energy in his senjutsu chakra than a perfected user; anymore natural energy than he could control and he would be petrified by that logic.
If he were to have just as much as a perfected version, then the 'inbalanced' bit would have to contribute to the partial transformation to a frog, since he wouldn't be able to use it in the same way a perfected user could. So, with all of that mixing in the water, his attacks would have possessed less natural energy than that of a perfected user's attacks of the same strength and scale.
Again, while the Path may be able to absorb a large amount, the Path should not be capable of absorbing an infinite amount without reprecussions.
P.S
http://www.mangapanda.com/93-440-5/naruto/chapter-435.html Crap visual quality, but the print is there. The Path absorbed too much of Naruto's senjutsu chakra and underwent petrification. Based on the visuals shown in the previous page or two, we're talking one of Naruto's entire sage modes.
As a sort of compromise, since it apparently took an entire sage mode (which in SL is like what, 3 turns of gathering natural energy?) to stone the Path, then the average sage technique is
safer (not entirely safe) to absorb senjutsu from.