but isn't the combat unit reassignment considered temporary?
The game doesn't state so we are safe to assume it is permanent. Anyway assigning valuable agents to front-line units is pretty much sending them to their deaths. Once you break down the operations and call off your agents the established spy network is lost for good. This can pretty much tell you that the reorganization was not what was going to happen.
Based on that conversation, the establishment of a new intelligence organization, presumably "Sith Intelligence," is heavily implied.
I just watched Youtube videos of all 3 possible choices. In all 3 instances the Minister specifically tells you that the Imperial Intelligence will not be rebuild. In both light side options the exact quote is "The Imperial Intelligence is not being rebuilt" while in dark side option it is "The Imperial Intelligence will not be rebuilt". However in dark side option he mentions a possible "Sith Intelligence". So again, it wasn't a reorganization but a start-up from a scratch (read the upper reply).
So now I can safely restate my main argument in this thread. It wasn't a reorganization but a complete dissolution of Imperial Intelligence with most of its personnel wasted and infrastructure destroyed. This is utterly ridiculous and stupid and there is no way Dark Council would approve that (reorganization and change of leadership yes, but NOT this).