Sorry, but you still haven't got this right. Stephanopoulos doesn't say he wasn't bothered by the Troopergate accusations. He specifically says he was bothered--sickened, in fact. Here's the passage:
When I asked Clinton about the rumors a few days before the stories broke, his abrupt shift to fast-talking lawyerly hyperexplanation mode convinced me something was up. "I never offered anyone a job," he insisted. But he didn't deny calling the troopers ... which gave me a sickening sense of déjà vu. I was back in Little Rock, hearing Clinton's voice on the Gennifer tapes. How could he be so reckless? He's so sure he can talk his way out of anything that he doesn't even think about the consequences. What if they have a tape? Why can't he just leave these things alone?
Stephanopoulos later says he didn't pay much attention to the "Paula" detail of the Troopergate story when it first appeared in The American Spectator because it sounded like Clinton had at worst made a pass at a young woman. He regarded this as inconsequential in comparison with the charge that Clinton tried to buy the silence of witnesses--i.e., the troopers.
I'm harping on this because I don't think you've come close to making your case that Stephanopoulos is being disingenuous. His claim is that he had doubts about Clinton's truthfulness from the time of the Gennifer Flowers and draft stories. These doubts compounded over time because of episodes like Troopergate. But if Clinton's answers were unconvincing, the charges against him were often ridiculous and never fully credible. (David Brock, the original author of the Troopergate story, has been apologizing for it ever since). Stephanopoulos thought what a lot of people did, that whatever Clinton had done back in Arkansas, he would have the sense to keep his pants zipped if he got elected to the White House. When he found out that Clinton hadn't had even that much self-control, he became fully disillusioned, and ceased giving the president the benefit of the doubt.
Why is that so hard to believe? The alternative would have to be that Stephanopoulos was an utter cynic who attached himself to a candidate he knew to be rotten because he saw a chance to get ahead. To my mind, that's much less plausible than the story he tells in his book.