It’s news to me that Twitch is going to remove raw IRC in favor of Websockets. I mean they even only just moved chat to new servers, including better support (SSL) for raw IRC as well, so I doubt they would get rid of it anytime soon. Also turning off raw IRC would break so many third-party tools (probably including any non-web apps of Twitch itself), so they’d probably need a really good reason to do so.
Maybe someone misunderstood something? I know when Whispers where introduced it was mentioned that they are going to move those off IRC eventually (although now they were moved to the new servers as well, so maybe they intend to keep them after all, which would make sense because a lot of third-party tools are already using them).
As for your issue, what extension are you using? I tried IRC via Websockets in Java recently and it worked as expected.