Actually, you have to follow the instructions of the ritual word by word.
So just do, what it says.
You dont have to actually click on the F4 screen on performing the ritual.
This is only the case for some of them, like the general sacrifice. For example, the "bear skull ritual" is also performed by pushing the bear skull onto a Pine(not a young one!) which is not next to another Tree, (although i didnt exactly investigate how "lone" that Tree has to be, but it worked just recently for me on a Pine that was like 6 or 7 Tiles away.
It is somewhat astounding how the game reacts when you just use your common sense. Yet it is unclear sometimes, if an action will have consequences.
For example, when i slaughter a deer for food, do the other reindeers standing near react to that somehow?
I have avoided that for the time being, just because of intuition. I slaughter them out of sight of each other, just as i would do in the real world...
what you report about your companion though, is a thing that should not happen in my opinion.
EDIT: On my new character, i still have to do the Waterfolk quest. But it is winter, so the first problem is to find a good Rock, and then (i think) you have to make sure all the water tiles around it gotta be NOT ice. Im not sure, but when i first met the water guardian, he was swimming.