Keep in mind that Reb Yochanan is the one who says in Shabbos, אם ברור לך כאחותו שהיא אסורה לך אמרהו, ואם לאו אל תאמרהו. He didn’t shoot suggestions.
I don’t really get the idea that to conflate ישו הנוצרי with בן סטדא. Nowhere does the Gemara put them together.
I’m every over occasion we purposefully do things to show apostates and heretics that we don’t follow their believes. What is different in this case that we buckle to the heretics?
My assumption is that there was a movement begun by ישו הנוצרי, a student at one point of רבי יהושע בן פרחיה. He was powerful and well connected to the royal family. There must have been many legends about him and he was likely very charismatic.
Then, about 150 years later, there arose this guy בן סטדא, who began a movement based on the previous one. He might be the famous Christian messiah, or perhaps he is Paul who spoke of this imaginary person and began a religion with that.
Either way, while we were not physically afraid of Ben Sitda’s movement and we composed litergical pieces to excise them, we were afraid the earlier powerful movement.