If you look at it from a fluff point of view, it does make sense, as Daigotsu was their very last hope of survival. And his terms were clear and absolute. The empress could not go back on her word without utterly disgracing herself and the Spider have been relatively well behaved up to this point. Also, anyone with the taint is turned into a Conqueror and sent to the colonies (well, everyone the Spider is willing to reveal, anyway, as most Dark Paragons are actually in Rokugan, but that's no different than before). The Taint itself has been turned into something "voluntary" by Daigotsu as he is now the new dark god. He ascended to take Fu Leng's place when the latter was killed by Kali Ma. It's still more or less all part of Daigotsu's plans, as he's even making Dark Fortunes and essentially making his original dream come true of an antithesis of Rokugan, only in a different way than he originally intended to. The public face of the Spider are their 10 or so courtiers from that new family they have (I forgot the name) and their monks, who have a rivalry with the Dragon that has yet to really turn into a big problem for either faction. As for the Taint being voluntary, people still hear the alluring whispers and the seductive nature of the power granted by it is still there, but you must willingly give yourself up to it (or under the strain of torture, as some Bloodspeakers have been doing to get a few Tainted minions).
It's very different from before, but I actually liked this resolution since I was hoping for one that didn't end up having every character I like brutally slaughtered. And it was a fitting end to Daigotsu's ambitions without him being utterly defeated. It wasn't quite what he wanted, but he saw his chance and took it. I just wish they had handled the transition period more clearly. More fictions were required to bridge the gap as there are too many important Spider characters who have just vanished. As the above posts states, we can likely assume they're dead, but how? These aren't just run-of-the-mill characters. Katsu has been around as long as Daigotsu has and has been almost as important to the Shadowlands' goals. The same applies to Chuda Mishime. It has been implied that he in fact remained loyal to the Spider until his death and it was his successor that caused the schism, but nothing is ever confirmed clearly. As for Omoni, there's no word on him at all, and that was a character that definitely needed some kind of end. The poor guy was so pitiable that he deserved either a confirmed death of sorts, or some kind of salvation and as far as I know, he has received neither.
The only important Spider to receive a more or less confirmed end is Michio, who apparently vanished and may have died in a glorious duel with a Fortune, whom he beat. Of course, this was told by Tetsuo, his successor as Grandmaster of the order of the Spider, to inspire a young student. He also stated there was but one witness, a blind old man, so who knows what truly happened, but considering the sometimes grandiose nature of the setting, it can be taken to be true that he did just leave on a last travel around Rokugan before dying in a duel or something along those lines. It's hard to imagine that guy getting beaten, however, since he was portrayed a bit over-powered (primarily due to his popularity, even outside the Spider clan).