While using the bio reactor i noticed that it's burning through seeds/food etc. extremely fast despite that i was only using very small amounts of energy at that time. I watched the generator a while then and it seems they are starting to burn everytime the internal energy storage is lower then 100%.

How about a treshhold instead ?
Internal storage < treshhold (e.g. 80%) => start generating energy
Internal storage = 100% => stop generating energy until it drops below treshhold again.

That way they wouldn't generate a ton of energy going to the void just because something used up 5 CF

I doubt something like that will be implemented in AA. But having comparator signal based on energy stored may be a good idea. You could then automate it with that.

That would work too, but would also require reactors to turn off when a redstone signal is supplied

I thought all generators already do the comparator and redstone thing. @Shadows-of-Fire you'll just have to do some copy-pasting it looks like

I checked the coal generator and that seems to work with redstone to turn off & comparator to read out state.
Only Bio reactor seems either to be missing some code or it's intended to work in another way: The comparator signal seems to indicate how many different foods are in there and badly a redstone signal supplied to the reactor does nothing. (so you can't turn it off)

edit:
Maybe the comparator telling you how many different kinds are in there currently isn't the badest idea. One could read out a battery loaded by the reactor and turn off the reactor when battery is full additionally to turning it off as long as there are less then 8 items in there. But what's definitly missing to realize that is the ability to turn it off with a redstone signal