I was just about to go and suggest this, good thing I ran a search first. I've been trying to think of any circumstances where running would break a puzzle or anything inside a building, but am coming up empty. No Gyms would be broken, no dungeons, other regions included whenever that happens. Heck, they even removed the whole "not being able to run inside" thing in later games. As far as I can tell there's really no reason not to lift this restriction unless there's something in the code that wouldn't make this feasible.