I also remember going through the prayers and being upset with what was said about him or to him or whatever you call it. But I asked our Nun Jenchang about it right after the prayers ended and she told me that he existed to help you get ride of poison thoughts and behaviors. Something like praying to know these thoughts and the pain they create - or rather he reminds you of the bad Karma that will happen if you do unkind things and such by creating pain in your life.
Anyway the way she explained it made me feel at peace with it. But I can tell you that when the prayers were going on I was very disturbed when it came to that part. I don't know anything about the other maleficent Budda's (I wonder why you call them Buddas?)
I also watched a video where Geshe Kelsang was asked if he was a Budda and he kind of said yes or maybe and that bothered me a little. He has done wonderful things I think by bringing Buddism to so many people. He has started well over 100 Buddhist centers and if it weren't for him I would not even be able to have a center to go to. The closest I came in the past was at the Unitarian Universalist Church when they had one man lead a meditation on night a week.
I really do not want to have any bad feelings towards this center or Buddhism in general. I want to be at peace with all of it. And I do remember listening to the Dali Lama say at a speech somewhere to not think your religion was any better than any other religion and that people come to enlightenment in many ways. And then he said something about cherishing your religion I think which is not a good thing.