Tim and Mia are, by this point in this verse, pretty much the best friends they've got (that aren't, well, Roy and Dick), *kills on DC's staff for taking away EVERYONE Tim loved that's not Nightwing (oh, wait. Canon Nightwing is ignoring babybro, too), and for never giving Mia real interactions outside the hero set* and they're very, very unwilling to have that messed with. Even by Tim's miraculously-ressurected soulmate.

And yes, Kon is pretty well overjoyed to be with Tim, and considers the brainbreaks a very small price to pay.

And no, they're not intentionally breaking Kon's brain. That's just a by-product.