You have to remember that Gotti's own life along with Gene's and Angelo's life were on the line due to the drug case. The only reason they hadn't been killed was because Dellacroce was alive. Dellacroce dies and less than a month later, Castellano hit goes forward. Paul was also vulnerable at the time due to his own pending trial. The timing was right.
Yes, According to Kurens and O'Brien in "Boss of Bosses," the other Dons were pissed at Paul because they had heard of him badmouthing them on the tapes the FBI made for Paul's RICO trial. Also, they were seriously worried that Paul would rat them out rather than spend the rest of his life in prison, away from his beloved Colombian housemaid. That's probably why Gotti got away with whacking a boss without the Commission's go-ahead.
