i am at a loss on how to comment on this issue because i do not have enough historical knowledge of what was going on in Tibet at that time. i have previously read that the Gelugpa had taken over other monasteries of non-Gelugpa tradition and converted them to Gelugpa. It sounds quite Christian to me and makes me think of whether this inter-buddhist lineage dissension is similar to the Protestant and the Catholic differences over the centuries which became so huge that great wars were created and much death ensued. Even in Northern Ireland, this difference is still simmering with occasional outbursts and destructive and tragic results, though it was supposed to have ended in 1998.
Anyway i digress. The point is that religion, because it is practiced by people, has often caused violence and disharmony among people. Perhaps in Buddhism, we are fortunate that there has been less violence than other religions, nonetheless, there have been points in time when there has been conflict, and today with the issues in Myanmar, it is worrying for Buddhism in the future. We are living in degenerate times i guess.
Personally, if i look at Pabongka Rinpoche and wonder if he was really schismatic, i think we can look at the 5 heinous crimes which would land any one of us cooking in a pot of oil somewhere. Pabongka Rinpoche obviously did not take a rebirth in a hell realm, which indicates to me that he was not schismatic and the fact that he has reincarnated back also proves without reasonable doubt that Dorje Shugden is a good practice.