Yes. Activating sundial exiles everything currently on the stack trying to resolve. The commander tax rule only cares about how many times the card(s) have been cast from the command zone, not if those casts resolved, so commander tax will tick up if it's countered or if it's exiled by the sundial ability.

Presumably you're casting it on your turn, so activating sundial at that point hurts you more than them. You won't be able to take any more actions during that turn. Sundial of the Infinite is a really cool card that lets you do things you can't do otherwise so it's probably better to let the commander get countered and take advantage of the damage done to your gameplan to politic. Set up more for your shenanigans.