As far as I can tell, the main issue with countering heimer is that people don't know how or dare to do it. They let you dig in, get your turrets set up, and by the time their teammates realise they need to gank you, it's too late.
However, once I do go up against a well coordinated team, I notice myself being shut down. They actually do early ganks, get me down, push me back, leave me no room or whatsoever.
Countering heimer isn't a thing you should try alone. You want your team to help you, as soon as possible. And don't stop after two ganks, or leave mid to gank on your own, keep doing it. Shut him down. Yes, in pug games this can be hard to do, for there are still people around that rather play their own game, but the moment you realise heimer is taking ground, it's too late.