Betting on games where you're actively involved in the outcome is a HUGE deal. Even with betting on some games, only for your team to win, it screws with the integrity of the game. Ranges from "I bet on this game, I'll put the beat-up player in the lineup rather than sit him" and "I didn't bet on this game, my best reliever can have the day off." Whether or not the manager has money on the game can have a huge impact on the outcome. That can't happen.
And it was always against the rules in baseball, it was never actually acceptable. If PEDs were always against the rules, and strictly enforced, and Bonds and Clemens were one of a few who took them? You'd have a better argument. But they took them because everyone else was, and MLB didn't care.