Except that when StackOverflow started it was a small startup with just three developers and a small user base. They probably made the decision early on to tradeoff any premature performance optimization with the ability to quickly iterate and ship the product by using Linq-2-Sql instead of hand-writing every single CRUD operation.
Now that their business (i.e. web traffic) has grown exponentially and have a larger group of developers they can now go back and optimize and performance tune the code including doing complete re-writes as necessary.
This is an important takeaway for anyone building a startup.