I think it's a great feature. It forces you to change your playstyle and not have some super-soldiers which you can rely on in every battle. The companion mechanic itself is really overpowered, so there has to be some type of drawback to balance it. You can't have your cake and eat it
I don't understand why people complain about this, if you want ez-mode just play on lower settings or put them in a separate formation and simple leave/retreat them.