The difference is that they didn't change how Feebas evolved, but they added another way.
You can't even attempt to evolve Feebas the old way in BW (so, logically, they didn't make Feebas no longer be able to evolve in the old way). However, if they changed someone's method of evolution, you could run into a situation where in the old games, he would have evolved. They also made it so his new way of evolution couldn't have been done in the old games for the same reason.
They can definitely change the level of a Pokemon's evolution, though (they might not ever realize this). Pokemon have different movepools depending on the region, so it makes sense that they could evolve at different levels depending on the region too.