Speed running isn't against the rules per se, but ultimately, SE gets to decide how they want players to play their content. Since SE went out of their way to curb speed running in a few instances, they obviously don't agree with the tactic.
However, I think SE stepped in because of how immature some of the community was acting over speed running. I think it's safe to say that most people aren't against speed running itself, but like to have a choice of when they want to do it or not. Of course, you got to have all of the "gotta have it now" section of players screaming at people to skip cutscenes when they're trying to enjoy the story, dropping parties when people who are either inexperienced or don't want to speed run are involved, and just being generally unpleasant.