We hold that (Avot 5,17):
כָּל מַחֲלֹקֶת שֶׁהִיא לְשֵׁם שָׁמַיִם, סוֹפָהּ לְהִתְקַיֵּם...
אֵיזוֹ הִיא מַחֲלֹקֶת שֶׁהִיא לְשֵׁם שָׁמַיִם, זוֹ מַחֲלֹקֶת הִלֵּל וְשַׁמַּאי.
Every dispute that is for the sake of Heaven, will in the end endure; ... Which is the controversy that is for the sake of Heaven? Such was the controversy of Hillel and Shammai.
I understand that G-d just loves those disputes as they all intend to refine G-d's truth (aka Torah). I also suppose that all disputes between R' Eliezer and other Chachamim had exactly that intention.
R' Gamliel decided to totally ban/excommunicate R' Eliezer and his views and explained it by (B"M 59b):
"גלוי וידוע לפניך שלא לכבודי עשיתי ולא לכבוד בית אבא עשיתי אלא לכבודך שלא ירבו מחלוקות בישראל"
Master of the Universe, it is revealed and known before You that neither was it for my honor that I acted when ostracizing him, nor was it for the honor of the house of my father that I acted; rather, it was for Your honor, so that disputes will not proliferate in Israel.
How banning most renown Sages and thus cutting the Halachic disputes can be considered G-d's honor? Isn't that exactly what G-d likes and asks us to do?