Disagreeing with someone is not sinas chinam. If it was, there would never have been a machlokes!
Despite their disagreements, many Rabbonim got along just fine, and respected each other. R’ Yoshe Ber Soloveitchik was respected by all the other gedolim of his time. R’ Kook was respected by the Chazon Ish, and he was also R’ Elyashiv’s mesader kiddushin!
The point is, you can say you disagree with someone in a proper manner, and still respect the person. When you decide to withdraw from a massive event which is supposed to show achdus because you disagree with the hashkafa of someone there, it is wrong.
I heard that in Israel, there will be many siyumim, one for each group. MO will have one, chareidim will have one, chassidim will have their own, etc. Why? Because they just can’t get along! I think this is terrible.
R’ Meir Shapiro said that daf yomi was intended to unify the different groups of Jews. Now it’s driving them apart instead.