This was always the thing comparing the Saints and deflategate. The Saints set up the bounty system, that was shown, and they were punished for it. It just so happened that it was shown that the players didn't really do anything about it, very few injuries etc. So they weren't punished.
The Patriots were exonerated by the Wells report, it is only Brady and the guys that supposedly deflated the balls that supposedly did anything wrong. If Brady is eventually found innocent, if the balls are proven to not have been tampered with, I don't see how the NFL can continue the punishment of the Patriots.