I respected that the majority of the players wanted the horde like behavior back. And honestly those folks would leave the clan as they would be just monsters not samurai at that point. But those that remain already have an identity. Kicking them out just because they were once out and you don't agree with that storyline isn't gonna end any better than having gone back in time even further and not letting the Scorpion come back from the sands. The oh I hate them and don't want them around cross armed stance has been huge...and it really kept me from returning the game for five years.
I actaully like the Spider and am fine with them sticking around... as long as we don't have to drastically change the rest of the setting to accomodate them.
Starting fresh with the LCG, Jigoku/Taint could be made part of the Celestial Order. An element of the world that must exist in balance with the rest. You can make it that Iweko upset this balance and to right it Tengoku and Jigoku bless Kanpeki's ascension to Emperor (wed to Miaka). No seals being broken, no conjoined realms, and a reason for tainted folk to exist within Rokugan and not as death demanding pariah. The Crab & Scorpion still have their walls to hold against the tainted nonhuman elements. You could also clean up the redemption/cleansing stuff that popped up out of nowhere and replace it with a single process that was discovered through thousands of years of experience and investigation by the Asako/Kuni/whoever else. No more miraculous cures that are discovered in 2 days that couldn't be found in 1k.
Another possibility is to give each major realm a Kami leader instead of 7 in Tengoku and 1 in Jigoku.
The problem with this and many of the other ideas, are that they expect drastic changes in the setting. Even sympathetic non-spiders would be alienated by these types of solutions.
Of course, there's precedent, since the Destroyer War went down that path. But I don't need to remind you how well that was received by the general playerbase.