This problem need not occur. The crunch is written after the fluff and is written to model the fluff within the expected scenarios.
If the fluff is well-written, it will also state the scenario the crunch is made to model and if you go outside it (which ideally should be corner cases only), then you know you need to go back to the fluff to understand how to make a new ruling.
It also very clearly explains why certain ridiculous inferences from crunch, when scaled beyond the limits of the model, cannot happen or have 2nd order effects. (auto-resetting traps anyone?)
I'm not saying we can just write fluff for all of 3.5's mechanics and call it a day. 3.5's mechanics are rather inconsistent and writing fluff explanations while keeping all the mechanics the same will result in painful contortions.
Rewrite from ground up is what I am suggesting.
To a certain extent, they ARE rules. They are rules that are given as a description rather than formal terms. Formal terms are only good in describing a strict model, but when you are trying to help give a baseline for dealing with corner cases or unusual scenarios that cause your model to break down, formal terms do not help.
Losing the ability for players to write their own fluff is an acceptable loss in my book. That sort of thing should be worked out with the GM ahead of time.
Well, that happens far too much. Especially since I can sometimes forget even my own rules if I don't have them laid out in front of me. The less I have to mod the system, the better.