I don’t know why you’d take a van this old to a dealer. They don’t have any special magic. They generally just charge more and try to sell you more. They also operate pretty much like any other shop would and I’d be surprised if you got a brand new compressor.
The bearing is in the pulley and would probably make noise whether the AC was engaged or not.
You could elaborate some more on the noise. You just said the “engine” whines - though I guess that’s not a precise statement in your mind. There are also lots of different kinds of whining.
If it is truly something that goes away once the transmission hits 4th then it might not be directly related to the A/C system, but instead to the load the compressor puts on the engine. Acceleration whine often comes from the transmission. But now we’re into needing a lot more info about the van. Has the transmission been replaced yet?