Honestly I agree. I'd be in favor of outright banning all emulators, because ease of cheating aside, there's all sorts of little inaccuracies like this that are too difficult to reasonably expect people to notice. I think a good chunk of the community is very very against that though.
Technically there's already a general rule covering this:
* You may use any emulator for competition; however, any action performed during the run (be it an in-game action or use of an emulator function) that cannot be replicated on console voids your stat.
That obviously doesn't help when the inaccuracies are small enough that no one notices them, though.
Worth noting Dolphin in particular is known to be inaccurate in ways that may or may not actually affect Sonic games. Specifically, it doesn't correctly emulate load times. That's significant for games like Metroid Prime 2 where some glitches depend on being able to get into position before a room loads; playing on Dolphin makes those glitches much harder to execute.
So maybe the solution is to verify that this is an emulation issue with Dolphin, and then ban it from competition until the inaccuracies are fixed? It seems a lot of peoples' PCs aren't quite good enough to run games in Dolphin at full speed yet anyway.