I don't think so...I think Deflategate went so badly for everyone, the NFL doesn't really want to go there.
Going back to the ESPN article, it seems like it laid out the whole story very well. The Patriots were videotaping and the rest of the league were sure the Patriots were guilty of all sorts of other things. Absolutely, Deflategate was meant to be a make up call -- Vincent even said prior activity was part of the punishment.
But, I think Deflategate WAS a set up...Not initially. When they saw the balls were down at 11.5 PSI they thought "All right! We got them!". Then, after a few days someone figured out the ideal gas law was the culprit. At that point, they hired Wells (and Exponent) to try to piece a case together. I have no doubt they told Wells what they wanted him to find because if this had been any other team, they would have dropped the whole thing.
The fact the NFL didn't (and still hasn't) let that one go, even after that major screw up leads me to believe they are thinking about this with their heads at all. So, anything is possible. But, the NFL backtracked pretty quickly on this one, so I doubt it.