We do both, depending on the situation. Consider those phonesets with BFTN's that you can't use a MOV command on. Often, for those, it is easier to swing the jumpers. And in my experience, people are capable of screwing things up in software just as badly as they can knock things loose on the frame. For moving ACD sets, swinging jumpers is the way to go, although I'm told with CS1K 7.5 you can MOV and ECHG to your heart's content. (But I admit I'm afraid to try!)
If you pay for a maintenance contract through a channel partner, wiring ports to live TN's at every vacant workstation is costing you money every month. If you have a predictable percentage of vacant workstations through the campus, you'll save money leaving those unwired to a TN, and just wiring them up at the frame when you need them. If ports and line cards were free, different story. I agree that IDF's should mainly be left alone, unless you're forced to split jacks or wire new workstations.
IMO, the best telecom techs are those who are equally comfortable doing it both ways, understand the pros and cons of both, and know intuitively which situations call for which kind of work. In both cases, accurate labeling and documentation at the jack, IDF, MDF, PBX, and in your own databases and/or campus maps is key.