What was done with Shinrarta should have been done with all systems containing important game assets. Most notably engineers. There should be no FCs allowed in any system in which there is an engineer. FCs only serve to make the engineering experience worse by clogging up system maps (although it is possible to tune them out) and result in those silly game crashes for people trying to take off from facilities.
I'm up for it, to a degree but disagree with the reason (disconnects). That needs to be fixed in isolation, irrespective of where it is. And it mostly has? I've not had any issues since the last patch but maybe I'm just lucky.
I'd be OK with engineer systems being no fly zones for FCs but it doesn't bother me that they're there. The system map should slot them into collapsed brackets (again, irrelevant where, just something that should have been sorted).
Permit systems make sense. Just not sure engineers needs it. After all, it's quite a benefit to owning a FC to be able to park it up in an engineer system to engineer more than one ship quickly. I don't think that should be taken away just for the reasons stated, when those reasons can be fixed (and should be fixed) without just going "nah, block Fcs".