You know what... Just do what you planned. it doesn't really matter if you call this thing reactor or whatever. Even if the model has such subsystem included, it doesn't mean that we have to notice that in main campaign for example (proper flags in .tbm?). If you would like to make a mission where for example, we are fighting against NTF destroyer and if you destroy this subsystem, then the Orion loose some hitpoints etc. No problem then, just modify the ship's table. Two minutes of work.
I've been always following my rule. "If you don't like something, don't use it or change it to make it suitable".