Lithium-ion batteries are perfectly safe to regen. You need to monitor the cell and pack voltages and limit regen under certain conditions, but it's well understood how to do this.

Any electric vehicle with a lithium-ion battery (and there are millions of them, from skateboards and scooters to cars and trucks) does regen braking. Without regen, you lose one of the most compelling advantages of having an electric vehicle in the first place.

In general, supercapacitors do have much better power density than batteries, but much worse energy density, making them impractical for vehicles at this point in time. There's a reason the vast majority of electric vehicles today use lithium-ion batteries.

Disclaimer: I was formerly a controls and systems engineer for a hybrid-electric vehicle company.