I've read a number of articles on this, and all said that he was tortured and murdered, with one being more specific than the others as to the findings:
1) several arms/legs broken,
2) not a drop of water in his lungs, indicating that he was dead before he hit the water,
3) signs of torture on the body,
4) his genitals hacked off.
Obviously (do I even have to say it?), #4 points directly to "he stood up against homosexuals in the Church and the priesthood."
Agreed, regarding #4.
In the one after-death photo I have seen, he was wearing clericals and the police had dropped a pair of gloves over his crotch, so I suspect that the genital mutilation story is true.