You just discovered that rims wear out from braking.
To reduce this effect in the future, you can choose high quality brake pads that don't embed grit into them. The Kool Stop salmon colored ones have a different compound with iron oxide embedded in (that's where the slightly "rusty" salmon color comes from). A word of warning, though: the Kool Stop salmons in some setups have a tendency to squeal, and the squeal can be so annoying that you might prefer traditional brake pads instead. For example, on my touring bike, I use salmons only on rear (the rear brake for some reason doesn't have a tendency to squeal on this bike) and Shimano brake pads on the front (I tested salmons on the front and they squealed like hell).
I also recommend using rims that have a wear indicator. Some rims have a deep groove. However, the groove can act as a weakener in the rim (it is a stress riser), so those rims having a deep groove wear indicator usually have a lot of supporting material and structures behind the groove to prevent the stress riser from failing the rim. This extra material increases the weight of the rim. Also, if the wheel is very accurately radially trued, the groove can cause the brake pad to wear unevenly, so that the brake pads have a ridge matching the groove, thus touching even the bottom of the groove.
My favorite style of wear indicator is used in DT Swiss TK 540 rims -- the wear indicator there is a small partial hole in the rim brake track in few locations. When the partial holes disappear, you know it's time to replace the rim.