“the Alter Rebbe tells us that if a bad thought enters your mind about another yid, even if you have a right to be upset (like Yosef with his brothers) you must immediately push it away bshtei yodayim and not dwell.on it as dwelling on it is an aveira.”
So it seems according to the alter rebbe the rebbe was committing an aveira with regard to Rav Shach and Rav Kotler.