It's not - the implementation of vanilla ship system AI relies on data already computed by the base AI (threat/ship state/etc), in addition to stuff that's passed in via the ShipSystemAIScript interface. I might add a way to retrieve modded system AI scripts to the API, though... but, your ship AI would then have to use/respect the ShipwideAIFlags that's passed in to the system AI script at creation.
Basically, system AI scripts, despite being plugins, aren't completely separate from the rest of the AI because they need to talk to each other to make more sensible decisions. In the case of core implementations, they are tied more directly for coding convenience and performance reasons.
Edit: or are you talking about the ship AI itself? The above is assuming you were asking "but can't we just stick ship system AI back in somehow?"