If most rabbanim today FORBID going onto the Har Habayit, why are those who advocate this practice not put in Herem?
As you write, most rabbanim maintain that one may not ascend to the Har Habayis area. However, the fact that other rabbis disagree is not (necessarily) a reason to place them in herem. If every halachic dispute would end with a discommunication, as in the tale of Rabbi Eliezer and Rabbi Yehoshua (Bava Metziah 59), there would be nobody left out of herem!
The concept of herem is a last resort, a tool of great power that must be reserved for people whose actions or words present a great danger to the public. Aside from such instances, we should recall that Chazal see certain forms of machlokes in a positive light (“these and these are the words of the Living God”), and even in today’s highly polarized society, it would be wrong to crush halachic pluralism, provided it does not cross red lines. The question of ascending to Har Habayis does not, in my opinion, cross any ‘danger lines’ that demand so severe a measure as herem.
[In addition, there is something of a cleavage in the political orientation of the rabbis who permit and those who prohibit, so that a herem would in any case not be very effective.]