It isn't just the aircraft getting tired in the Harrier fleet - its the crews as well. They have been on the verge of breaking for some time and indeed by some criteria are already broken. A large portion of the Harrier force have very little experience of anything except CAS in a benign environment ie Afghanistan. Obviously I mean benign from a medium level FJ point of view not a squadie on patrol point of view. Some (most of the army) don't have a problem with this - they believe that the RAF should only be doing CAS and ISTAR (and AT, AAR etc) for evermore, but the RAF standpoint is to maintain a flexible capability on top of the current operational tasks. A debate for another thread, really.
Typhoon is, of course the crux of it all. At the moment it has a horrible reputation in the RAF - CR(airshows and N America dets only). In terms of CAS capabilities it needs more weapons clearances - having the option of a 1000lb bomb or a different 1000lb bomb isn't very flexible.
For air to air it might have some issues but for the current UK ADR policing and FI roles it would be fine. So cut F3 and Typhoon takes over seems an obvious choice. Unfortunately the current commitment of the FIs, northern q and southern q is a big demand on aircraft numbers and crews. If Typhoon were to take on all 3 commitments tomorrow it could cope BUT the ability to gain other capabilities (such as robust CAS) and the spare crews for a sustainable deployment would not be there - and surely that should be the focus, both militarily and politically. Of course the Saudi buy and training does not help from a military point of view - although it has saved our ass from pretty much every other point of view!
I think the above is pretty much fact. My personal view is that the Harrier force are in 2 minds - they love being on ops and "important" (don't we all) and are a bit worried that once they have no operational commitments they will be sidelined and possibly cut. On the other hand they are a bit fatigued/pissed off with the constant Afghan deployments.