I don't see how they could prevent it or that it is an attempt to circumvent anything. Going with what we know or has been alluded to the Packers were going to trade Adams to the Raiders for #22 and Waller. For whatever reason, maybe because of Adams being franchise tagged, the league said no, you can't include a player (Waller) in the trade so the Raiders said we will give you #22 and #53 (or whatever it was) instead of Waller . The Packers said OK and the trade was made. Now the Packers want to trade that #53 to the Raiders for Waller. I Just don't see anything wrong with it. This is simply a player for a pick swap and nothing more. The fact that it gives the same result as a previously denied trade is irrelevant IMO.
As far as is Waller worth it, I say absolutely. Is TE a need? Not a huge need but if you can upgrade your TE from Tonyan to Waller, and I see it a as a big upgrade, plus you get to keep Tonyan its definitely worth considering. I'd like to see 2 bonafide pass catchers in the first three rounds (5 picks) assuming they still pick a rookie WR in the first this would give them the second and they wouldn't need to draft another. They still have 3 other picks to address to other areas you are concerned with. If you are looking at it from a BPA standard you would have to ask is Waller better than any player you could draft at #53. He was ranked as the #35 player in the NFL last year (a subjective ranking I know) but I would say yes, he is better than anyone you could draft at #53. If you are looking at it from a need standpoint like you said, TE isn't a huge need but its an area that could stand upgrading. As many say you arrange your big board in tiers. if 2 players are in the same tier you look at the position of bigger need but if a player at the position of lower need is ranked in a higher tier you go with him. I think Waller would be in a higher tier. I think the only advantages to a rookie at 53 over Waller would be he is younger and would be cheaper. Now granted those aren't small advantages but I don't know if they would be enough to go with the draft pick.
Of course if the Raiders say no, as I suspect the would, its a moot point. On top of that I kind of question the veracity of the report or suggestion that the original deal included Waller. I'd think the Packers would have been aware enough of the rules to not try to push it through.