I think that while it is important for the league to be on top of how they procure a consistently performing baseball, and as such, may recommend changes to the baseball, or the manufacturing of the baseballs, I don't believe that anyone in the league office has put their thumb on the production in such a way to manipulate how the game is played, or enjoyed by fans. Everything that I've read over the years seems to demonstrate that the league wasn't any more educated on ball-flight patterns over time than the public. Or, at least, not any more capable of affecting a change to the ball with foreknowledge of that change's impact on ball-flight, excepting generalities.
I'm not sure why people constantly presume conspiratorial malintent with the league office, or for that matter, any administrative oversight by organizations/institutions.