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.
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).
Imperial Intelligence as we knew it is not being rebuilt, but the DS and "Batman" ending both seem to indicate a new Intelligence is coming into being with the DS IA being in charge of it.
The game may not say that the combat re-assignment i's not temporary, but it doesn't say that it is permanent either. You know what they say about assuming. If you choose to perceive it as permanent, well that's up to you.
Sending Intelligence agents in combat situations isn't a death sentence nor is it unheard of, all major Intelligence agencies have paramilitary units that operate in wartime conditions and NOCs and other field agents aren't exactly sitting in cushy offices, eating ice cream and playing hopscotch.