Exactly. The 'downgrade' from Jones to Long for the money saved, take a flyer on Cooper and get a #2 in a year you were down a pick. For all we know the synthetic weed thing made taking Cooper and his salary a prerequisite to getting a 2 instead of a 3. I don't imagine that sat well with BB and it certainly must have lowered his trade value at least a little.
The synthetic weed thing is the X factor - maybe they decided they didn't want Jones on the team this year, period, in which case it's hard to complain about the haul they got.
BTW, there's no reason to put "downgrade" in quotes. Jones has four sacks this year, Long one. Since Jones entered the league in 2012, he has 40 sacks, Long 25. Sacks aren't the be-all and end-all, but at this point in their careers, Jones is a significantly better player. Arizona has the second-best sack rate in the NFL; New England is tenth-worst.
One other note: I like Thuney and Mitchell, but they didn't trade Jones for Thuney and Mitchell - they traded him for a late-second-round pick (and the negative that was Cooper), which is like a 45% chance of being a useful player. It's great that they turned that 45% into one and maybe two useful players, but that's not really part of the Jones trade. If they had used the second on KeiVarae Russell instead, is that a worse trade? To me, on the field at least, this is a poor trade to get just a second-minus for Jones, but a great use of the pick they got (both trading back and getting Thuney / Mitchell).