I was wondering if it could be related to this plugin that the helicopter often goes higher and higher after killing his target once.
It goes so high it cant be shot anymore and then just flys away.
Did anybody else experience this?

Sounds like it's simply starting it's egress (flying out of the map) it flies out of the map after 15 minutes and delays this if the helicopter is still in combat. So if it kills the target it will no longer be in combat and start flying out of the map (which starts with the helicopter raising in altitude so that also fits in with your description)

No. This doesnt look like normal behaviour. If it is about to leave the map it may go a little higher before leaving but what I experienced was that it flew many many times higher than normal before leaving.

Sounds like a bug, for sure, but I don't think it's related to HeliControl. Should be easy enough to find out, though. Try unloading HeliControl and callling in a Helicopter through one of Rust's commands (I think it's heli.call and heli.calltome) and see if the issue persists.