One of the attractions of this website is the openness of the rules compared to other similar websites, the so-called "honour system" or what have you. Lose that and this website loses one of its USP's. However, with things the way they are, I've always felt an undercurrent of mistrust throughout the community that from time to time, gets proved right when people are caught out.
For this reason, if it can help give this site's records a bit of authenticity, and give people more peace of mind, then I would say that I'm for this move of banning emulators with TAS features, as long as there are enough emulators out there that people are still able to use them to compete in all the games they are currently commonly used to compete (Genesis, Game Gear, GBA I would think being the crucial ones) on the main OS's. Make the rules too restrictive and we risk sucking the life out of the competition on these games, but I would have thought the necessary emulators do exist (With Fusion being given as the example that works for Genesis and Game Gear).
Obviously I'm against the retrospective removal of stats using the banned emulators - that would be total chaos and would also involve the removal of pretty much all of my Sonic 1 stats, done using Gens (though if I TASed those stats I did a pretty horrible job of TASing). SonicBoom mentions another TAS rule that says "Note that if a new rule is enacted, anything already submitted in violation of that rule is void.". What this proves is that to every rule there should be an exception, and this is it.
So my opinion is, make sure that enough viable emualators exist such that we're not essentially banning emulators here, and then go for it. This is a small (and obvious) point, but I would say it would be far better to have a whitelist of legal emulators rather than a banlist if this is the way we choose to go, for practical reasons.