and I'm talking about what SEL means to me.
I think that you're making it out to be anti-Wired in some way. As if The Wired entering real life was a problem. It doesn't seem like that to me, it seems like the show portrayed the birth of a god, which is a messy affair. Lain is fractured between her meat-self and her wired-selves, and then there is also Masami and the Knights who try to control The Wired, which Lain is the god of. Over the course of the show she comes to understand herself more, and to unify her self into a cohesive being. Out of love for humanity, she uses her powers to remove herself, fixing all the ills that her birth caused.
The show's tagline is that "everything is connected". The Wired is a tool, yes, but there is no indication that it is removed from the physical world at the end of the show. The fact that Lain is able to project herself into the physical world to talk to Arisu again shows this. It's just that Lain is no longer fractured and Masami is no longer causing trouble.
I think the real "message" of the show, besides the baseline feelings it evokes, are that The Wired connects us, but rather than turn that into a solipsistic "The Wired is the only thing that is real" viewpoint, it connects us as real people, and that when we put on fake faces on The Wired we are trying to reject this connection and it causes bad stuff like, say, the alt-reich. How many of those kids think they're being ultra badass anonymous internet warriors by posting racist memes, I wonder?