The best way to balance grenades is to make them rare, really rare, so that players usually only use them in kind of emergencies and not spam them.
Gotta disagree there. As a main rogue/thief player myself, grenades are important for offensive and I want them to be abundant in quantity. As for balance, you can tweak the radius, distance, damage, special effects, items required to craft them, their price, skills needed to use them, but one thing that hurts the rogue/thief is not having access to them.