I'm not so sure about that. One of the few good things in Best Wishes was the fact that Team Rocket appeared so sporadically. And when they did appear, they were serious and actual threats. When BW2 came and they reverted to their idiotic selves is when things really started going downhill, both for them as well as the rest of Best Wishes. Before Decalore Islands, the saga could have been salvaged. Right now, they're only taking up space and some of the best episodes in XY are when they are absent or are not really doing anything that interferes with the Kalos quartet. If they left, either by quitting Team Rocket or, like this would ever happen, them going full evil and being killed off, I would not miss them. The irony is that if they are written off, I would rather them go full evil and get killed off for real, having them go out memorably, than just blasting off or quitting TR without much buildup.
They have tons of fans in Japan though, so those people would miss them. I certainly wouldn't bat an eye, but I would feel bad for people who like them at least.