Why they changed the ending.
This movie was was much darker than the book was. The book blamed everything on Cutter, a rogue and naive naval officer. The film was a conspiracy inspired by Iran-Contra. The death of Felix was the death of Pablo Escobar which had not yet occurred when the book was written.
Also, this was about the time that the American public was catching on to the fact that the US government had something of a working relationship with the Colombian drug cartels. The book was kind of an apology for this fact, blaming it all on a few unethical individuals looking for career advancement and revenge. The film showed that it was much more than that. It was an ugly choice, but the best one given the circumstances.