Popa,
While I agree with you that tzedukim did hold of some sort of Torah Sh’bal Peh, there is no way that they were not clear separate groups during bayis sheni. Tzedukim were considered apikorsim during Bayis Sheni. I haven’t read the article you are referring to, but it does not fit with numerous gemaras.
At your suggestion I will spend some time reading Rabbi Linzer’s blog (I didn’t know he had one). But for now I will say that although I don’t know Rabbi Linzer personally, every time I have seen him he has been holding a sefer (usually a gemara), and whenever there was a spare moment he was learning. I don’t know what else he may be, but the man is a Masmid.