I think it rather depends on exatcly what is being done, and why.

Let's consider the example of someone making a mistake such that they take off with reversed ailerons. Perhaps the pilot is able to keep the aircraft somewhat stable in the air such that it is not an immediate danger to all around (i.e. it does not need to be dumped for the safety of spectators or others), but the pilot knows that he will not be able to land the aircraft set up as it is. As long as the reprogramming to reverse the aileron channel can be done with the model suitably distanced from anyone who might get hurt if anything else goes wrong (see below for an example), I see no reason why the reprogramming attempt should not be made (by a helper - not the pilot) - any crash caused by making another mistake would presumably be away from the crowd and be no worse a risk than if the pilot had elected to "sacrifice" the aircraft the moment he realized that he had a problem. Now, ideally we would not ever get into a scenario like this, but on the basis of developing contingencies for various "what if" scenarios as my RAF instructor used to drill into me, this would seem like a course of action that has a chance of improving the odds for a successful outcome to a flight gone bad.

BTW, I have actually seen an instance similar to the scenario described above, and the story in this case was rather amusing. In this case though, we have a recently soloed pilot on his first low-winger, let's call him Fred, then we have the club VP - Jerry.

Fred : This low-wing stuff is harder than it seems ... I can turn left ok, but my right-hand turns suck. Can you come out and help me figure out what I'm doing wrong?
Jerry : Sure - take it off and show me exactly what you mean, then I'll know where you need help
Fred takes off, demonstrates circuits in both directions, wit the left ones being ok and the right ones being barely survivable. Jerry now takes the TX to demonstrate the correct way to do things.
Jerry : Holy S**T !!! Your ailerons are reversed !! Didn't you realise that ???
Fred : No - I guess I just kinda move the sticks one way, and when the model goes the wrong way, I move the sticks the other way.
Jerry : You're right - you are flying purely by reflex, rather by conditioning like I am, so it seems more natural to you. Given that you've been doing that for a couple of flights now, you need to take the airplane back and land it - your reflex approach means the aircraft can survive until we get it down & fixed, whereas I'd probably just stuff it at some point in the approach when habit takes over if I try to land it.
Fred : No Way Man !! You've got me worried now - I can't handle that - YOU need to land it for me.
A couple of minutes of such arguing continues, with Jerry concentrating incredibly hard to keep the aircraft airborne and away from the pits, then Fred has a stroke of genius...
Fred : I know - there are some switches behind the battery pack that let me reverse the channels. You keep flying the plane and I'll pull the battery out to get to the switches, and all will be well !
Jerry : WAIT ! For heavens sake make sure you don't disconnect the battery by pulling on it to hard !
So Jerry's standing there holding the TX at about waist level for Fred to get easy access, while Fred kneels down in front of him and pulls the battery out, and brings his head in reallyclose so that he can read the lettering on the inside of the back panel. Meanwhile, the people on the sidelines don't know what's hgoing on and just see this standing/kneeling combination which looks just like the scene from Police Academy where Commandant Lassard is standing at the Lectern and a young lady who is hiding in there starts providing certin services to him.... !
Fred : Hmmm - channel 2 or 3 ? ...
Jerry : WHAT ?? If you don't know then please ...
CLICK !!!
Jerry : WRONG ONE !! You JUST REVERSED THE ELEVATOR !!! AAAH JEEZE ....
Jerry is now almost biting his tongue off with the sheer concentration of handling reversed ailerons AND reversed elevators.
<pause>, CLICK, <pause> CLICK, then all is well and the model lands ok but Jerry is unable to move from the flightstation for a couple of minutes due to his suddenly weak knees.

The above is a true story from the SCCMAS Tomcats club.

Gordon