Why can't we Counter Jungle Krugs?

I believe the timer is on the Ancient or Big Krugs. But someone could have simply killed them.

The camp takes a long time to finish, so the idea is to allow junglers to kill only part of the Krugs if they want to leave quickly for a gank or for preparing dragon.

Just take the whole thing. You've already done the hard part, so take all the exp and gold. Do this for all their camps actually. By the time the camp respawns, you'll be so much stronger that you can just take it again.