That is a potential risk, yes. But there should be enough tadpoles around to not really need to harvest those of the companions I'm keeping, and I don't think Larian would take away agency too much even though it might have made sense.
I wouldn't really assume that, if I recall correctly, Swen emphasized a lot that you might end up all alone if you focus entirely on increasing your power. That could mean that your companions leave because they disapprove of your actions, or that in order to achieve that power you'll need to sacrifice them, maybe you need all the tadpoles available for the final unlocks of the illithid skills tree.
