The rape charges helped to chip away at his character, isolate him and erode popular support. It's not hard to believe that intelligence services could do something like that. That's their MO.
It is possible for Assange to be a bad guy and also for the U.S. going after him after all this time to also be unjust and bad. Not everything is a conspiracy and you don't necessarily have any "good" people when you start messing with international espionage and related areas.