How do you understand the halachik process of the difference of opinion between R' yochanan and Bnai Biserah. Why was it permissible for R' Yochanan to seemingly mislead Bnai Biserah into thinking that they would discuss the issue afterwards only to be told that there was now precedent?(I realize one could say that technically he told the truth since they did discuss it but.....)
Good question. First of all, your own answer is good -- they did discuss it, and Rebbi Yochanan's conclusion was that there was nothing to discuss. Second of all, Rebbi Yochanan [ben Zakai] was the leading authority of the times, whose opinion was the final one, and he was fully authorized to rule counter to their opinion (and they would be required to follow his opinion).
He could have discussed the issue first, heard out their argument, and then ruled in accordance with his own view, but instead he opted to avoid a controversy and to push off the discussion until after the Shofar had been blown. For the sake of peace and avoiding controversy, this type of "misleading" is certainly permissible. Bnei Beseirah, too, knew that their view was subordinate to Rebbi Yochanan's ruling, and that is why they acquiesced to blow the Shofar first and then discuss it.
See also the CHIDA in PESACH EINAYIM to Eruvin 67b, who discusses your question. (He says that although the Gemara says that "first you do the action [of a Halachic decision], and then you can ask questions on it," that does not apply in a case in which the action was seen or heard by many people (such as the blowing of the Shofar), and thus Rebbi Yochanan was justified in not discussing the matter after the act was done. Bnei Beseirah, though, had to acquiesce to do the act, because of the principle "first you do the action, and then you can ask questions on it."
In addition, asking questions after the act was done applies only when one thinks he has a definite refutation for the act. In this case, Bnei Beseirah were only in doubt whether or not the Gezeirah not to blow the Shofar on Shabbos applied in Yavneh, and once the action was done, there is no requirement to discuss doubts about it.)