The car isn’t going to let you shift so early that you’d overspeed the engine or anything. The whole point of downshifting is to get, as you say, the car to pull to slow down. If you don’t want to feel that, don’t downshift.
I find most paddle/automanual shifters to be pointless unless it’s a dual clutch transmission. Which is not available on the Civic - only on its Acura version, the ILX. Normal manumatic shifters are too slow to react, and half the time the computer overrides what you want to do anyway (second gear starts on ice are not possible in many auto-trans cars with paddle shifters/sport sticks, for instance).
In short, if you’re doing it for fun, don’t worry, you won’t hurt anything. If you’re doing it because you think it’s necessary, it’s not.