Only in the most superficial sense. No, they didn't have him put on the blue suit and the cape, and they didn't have him fly, but those are minor trappings. In every other respect, they were writing a Superman show those last 2-3 years. I mean, my God, we saw the formation of the Justice League, we saw the Legion of Super Heroes and the Justice Society, we saw the battles with Doomsday and Darkseid, we saw Cadmus and the Suicide Squad, we saw Clark share his secret with Lois and all but marry her.
None of that was the original intention of the show. The original intention of the show was to revamp the story of Superman's origins in a way that would fit the mold of a WB teen drama, that would stay as far as possible from the comic-book roots of the story in order to make it more palatable to an audience that wasn't into comic books. (The same philosophy generated The WB's short-lived Tarzan series in which the entire show took place in New York City, Jane was a cop, there was no talking to animals, and the name "Tarzan" was only spoken once in the entire series.) "No flights, no tights" was originally more of a metaphor, a symbol of the overall mandate to reinvent the mythos in a more mainstream form and avoid the more fanciful four-color aspects of comic-book storytelling. And it worked. In its heyday, according to anecdotes I read at the time, there were people who became fans of Smallville without even realizing that it had anything to do with that Superman guy from the funny papers. To them, it was just a teen drama about a guy from another planet, Dawson's Creek meets The X-Files.
By the last few seasons, that was clearly no longer the case, for two very good reasons. One, movies like Iron Man and Batman Begins and The Incredibles had made superheroes hot, so the original belief that a comics-based show had to divorce itself from its comic-book roots to succeed no longer applied. Two, because the series ran so much longer than expected, they simply ran out of stories that fit the original paradigm of the show, and so they had to throw in more and more characters and storylines from the comics in order to keep going. So while "no flights, no tights" was originally a shorthand for a much broader agenda to avoid comic-book elements as much as possible, by the last few seasons it had eroded down to an arbitrary and extremely narrow restriction on exclusively those two things -- Clark wouldn't fly even though multiple other characters could (Supergirl, J'onn, Hawkman, etc.), and Clark wouldn't wear the tights even though multiple other heroes wore colorful costumes. So even though it was expressed in the same words, the meaning of it had changed profoundly. Originally it was the defining storytelling philosophy of the whole series, but by the last couple of seasons, it was an arbitrary restriction that had no real impact on the way the stories were told.
He already was Superman in every way that mattered. He was teaming up with the freaking Justice Society, battling Zod and Darkseid, working as a reporter at the Daily Planet, and engaged to marry Lois Lane. He had a dual identity, he had a superhero nickname, and he had a special costume he wore when fighting crime. They just weren't the nickname or the costume, but that's a trivial distinction. (And sure, he could only run fast and jump high rather than flying, but the same was true of Superman prior to about 1941, and I think it's true of the young Superman Grant Morrison is currently writing about in Action Comics.) Functionally speaking, in every important respect, these were stories about Superman. So don't tell me the producers didn't want Superman on the show. They had Superman on the show, or as close as they could get given Welling's unwillingness to wear the glasses or the tights.
