Why would the Jedi treat the clones 'badly'?

Jedi are a lot of things, but cruel asshole bosses is not one of them.

Pong Krell was a fallen jedi so hardly indicative.

If the clones were "free thinking" then more would have been won to the jedi side than was depicted. Sidious wouldnt take that risk and would instead have used something like the control chip which doesn't control their whole lives, but waits as a triggered device that turns good troopers into mindless machines focused on one thing.

The troopers have no idea it's in their heads and they have no notion of sidious until it is triggered.

I'm more with the cannon chain of events. It plays up sudious's evil and heartlessness while taking intent away from the troopers entirely. The EU version makes the troopers complicit in that they have to choose to obey an order when they know their Jedi's are good commanders and loyal.