I'm very new to this game and i have a Biofuel Reactor in my base.
When i put fuel in it, is there a way to stop it again?

Short answer.: No.

Four days, no answer. That's because nobody knows for sure - we don't use it anymore :P

This thing could be helpful if only we could control the amount of fuel we pour into it.
(LIke, pay 10 oxygen to activate the teleporter.) But we can't.

A workaround would be to fill all my oxygen into one exocraft, take 10 back, change to another exocraft, and then operate the biofuel reactor. Just putting the first exocraft out of reach doesn't help. The game helpfully considers all available inventories.

I guess it's really only meant for filling up a battery in emergency situations. Like, I have miscalculated the power use of my base, batteries are dry, and I need to bridge the night.

As Jentuncegs noted: no, there doesn't seem to be. Its a poorly thought out addition on HG's part, IMO. You're far better off just building a solar panel and battery