What the repo contains should not be very relevant. Proprietary and GPLed software can be in the same repo/disk/etc. We even see this in the official git repo with non-free firmware. Instead the concern is about what code the terminal application ends up using and what it links with. If his terminal did not link to any weird stuff then it is probably the case that they could avoid it as well. Also don't forget that the GPL contains an exception for system libraries specifically.
As for the segregation policy, it sounds like a self-imposed problem.