hmmm...?? What was it that nullified his jutsu from attacking naruto any further? Potato chips? He manipulated gudodama's shape and used it to nullify Madara's jutsu...When has a mere gudodama done that?
1. Onmyoudon doesn't work on Senjutsu based attacks, which all of a Juubi Jins attacks are.
2. The lightning was not erased, it was simply held back in a similar fashion to a lightning rod.
3. The lightning actually stems from the Rod back down into the ground, and actually slightly towards Naruto.
4. A similar Senjutsu Raiton attack used 2 pages later cut Naruto's Gudoudama rod in half.