Hell, we already realize that all of our thoughts are happening through a blob of firing neurons. I don't see why understanding it would make anyone feel different.
If anything, we could get some bad-ass ghost in the shell cyborg implants and bodies so we could talk wirelessly without physically speaking, personally see through cameras across the planet, use robotic limbs as our own, or live forever (as long as machines can keep a brain alive without a supporting organic body) <3
In that sense we could also have virtual reality that literally takes over our senses. That would make video-games and hands-on training awesome. You could learn to paint without actually using paint. Sports might even be fun if the game strategy and control is decoupled from physical prowess. We could be having this conversation "face to face".
Or.. give us all a hint of autism. The kind that allows savants the ability to do math on huge fucked up numbers in their heads or remember everything they've ever read.
At the very least we could tune chemical imbalances.. It's not really changing their sense of "free will" as it is regulating their mood. They can do what they want, but they wont go on explosive or psychopathic killing sprees.