From what it looks like, this is quite literally the ability to get code into the main codebase with no oversight. Even without malicious intentions, it seems very easy to do something awful by accident.
The most awful thing that could happen to 2006-era YouTube: they could stop delivering ad impressions for an hour or two. Oh wait, no; 2006-era YouTube didn't even have ads yet.
That said, the people with this access probably knew WTF they were doing.
And it sounds like it wasn't just DOS - also just plain "it doesn't work in ie6" seems the most likely outcome; crashes and DOS that the article describes just sounds like the most egregious cases.