The implication was never that the Brotherhood are slavers, but that they have shown they are willing and able to use fairly underhanded methods to force cooperation from individuals when and where necessary. The Brotherhood does what it feels it needs to do, with the needs of the collective taking priority over the needs of the individual.
In the situation in question, they put the collar on you to make sure you can't get away from them and give away their location until you have proven your worth. If you walk away to tell the Wasteland about the Brotherhood, POP! off goes your head. If you cooperate, the collar comes off.
If you wanted to utilize the remnants of the Institute to help the Brotherhood and its technology addiction, I can see the Brotherhood putting an armed guard around and collars on Institute scientists to make sure they continue to work for the betterment of Mankind. You know, for the whole of mankind this time. Not just their special underground gated community and a bunch of synths*. At least they're still alive, and still TECHNICALLY doing what they said they would - making life better for people. If they decide that they don't want to help humanity, that's an unfortunate loss. Bl
* I feel that Gen 3 synths count as humans in a mental sense. They feel emotions, they react, they bleed. However, they cannot replace humans as a population - mostly because they probably can't reproduce. And if they COULD reproduce, imagine the genetic bottleneck that would create. They are not the 'future' of humans for this very reason. They can plug gaps, but they cannot replace flesh-and-blood grown-in-the-womb humans.
The whole scenario is pretty dark grey as morals go. But look at it this way - what's more morally wrong? Nuking them to oblivion, or letting them live and continue practising science for the Brotherhood? Is forced service (in good conditions) worse than death? It's not like they've been sent to work on farms, just continue some of their projects for a new organisation. It's an interesting point of thought and debate, something that fits in the morally grey Fallout world. A world that likes to kick you in the teeth for doing what you thought was right.