I also cannot speak for Rav Shmuel and the wzo, but those who allowed it did not say that zionism is any less bad than it used to be. They said that it was a token statement affirming zionism.
Most gedolei yisroel were extremely against that psak, as we have a mesorah from all the gedolim to not join the wzo; in fact, this was a major element of Agudah’s shitos.