If braking is causing the whole bike to actually wobble something IS wrong.
It could be the wheel isn't seated properly in the dropouts. ?? Check out the parktool website.
If you had a bike shop do the work you should take it back and see what they say about it.

- "Your mtb tires had more rolling resistance & were essentially slower than your new hybrid tires are now. So the braking force necessary will now be greater than before to slow a faster tire down."

How can the braking force be greater? won't it take the same force to stop (same speed different tires) unless you change rims &/or brakes?
Yes, smooth tires roll easier than knobies, if the rolling resistance with slicks is less, wouldn't this also lead you to believe it woul grip better during braking under ideal situations?