While Lin Fan would have preferred to keep these experts alive since turning living humans into puppets was always better than using corpses, he couldn't do that in this situation.
Who knew how long it would be before the Hunters Organization acted and if they were to ask for these experts from Lin Fan, Lin Fan would find it hard to say no.
They would be hidden dangers for him if they were released, so instead of having that possibility, it was better to kill them all off now.
As for why living beings were better than corpses, living beings still had wills even after being turned into puppets by Brainy, so they could still think for themselves. It was much better than having mindless puppets that Brainy would need to control itself.
But the problem was that it would take too much time since Brainy couldn't forcefully turn the puppets. Or if it did, it would take a while to corrode the mind of these experts.