This comes down to two problems:
1. are hacking outcomes moddable in any way except changing the prerequisites?
2. would it be possible to enable Sleepers, Sleeper abduction and Sanctuaries on Academy systems, at least for Umbral Choir?

Academy systems have proper population information so they should be able to handle Sleepers correctly (I guess the problem was it means one could steal resources from the Academy empire after meeting the Sleeper thresholds). I wonder if something could be changed about the Academy empire file setup to make their systems be treated as regular major faction ones.

Also, does the Academy even attempt to trace the hacks back? The files suggest it tries doing so without the Awakening and even tries to hurt heroes on major faction systems. The expanding version of the Academy seems completely passive in that regard and as an Umbral Choir addict I'd be more than happy to change that.