It didn't work. There just weren't enough of the new Legion practitioners, and they didn't have time to get good. A six-week boot camp in an Arcanos simply couldn't compare to the decades/centuries of training the Guild members had. So there were immediate shortages of skilled soulforgers, pardoners, and other vital trades.
Further, the Guilds had always been very secretive about their membership - many members came through the Breaking untouched. And with their superior skills and equipment, they were able to set up a thriving black market. One that even many "loyal" Hierarchs routinely turned to.
So Charon had a problem. The Legions couldn't meet the market demand, but the Guilds could (and actively were). But he couldn't just pardon the Guild members . . . And yet Stygia might well fall without their skills.
The compromise was sort of a licensure system, coupled with de facto amnesty. "Reformed" Guild members were allowed to openly practice their skills again, as long as they endorsed the party line - that the Guilds were disbanded. In exchange, the Hierarchs would ignore any "innocent gatherings" that these "ex"-Guild members decided to attend.
So in the modern day, the Guilds officially don't exist. And newly Reaped wraiths aren't told about them. But any Hierarchy wraith with an interest in history, and a taste for politics or conspiracy theories, will probably quickly notice that the wraiths with advanced Arcanoi talents spend a lot of time at "private parties" . . .
Edit: In other words, (almost) all Guild members are also Hierarchs, and thus belong to a Legion. At the same time, they're a member of an illegal union slash secret society slash professional trade organization slash crime syndicate, one that has its own agenda and resources. Not every skilled Arcanoi practitioner belongs to one . . .but the better the practitioner, the better the odds. And the better you get, the more likely an invitation will be extended to you.