Unless you have a very good reason you just shouldn't change what a user has entered; just trust the user's input where there's no security or integrity reason to do otherwise. This example of Twitter messing with user input and breaking things is a good example of why you don't do that.
Remember that the problem here is purely a performance optimisation having become a pessimisation; it’s not actually breaking anything. I tend to agree with you, but only as far as functionality is concerned: that you shouldn’t act otherwise than the user specified. For display, I’m quite happy with dropping https://, and not too distressed about dropping www.. But for my comment, I wasn’t talking about changing what the user entered, but rather being willing to accept either of the two most common forms that users may enter.
Entering www.example.com and getting example.com is a breaking change in the sense that you wouldn't expect the user's machine to make a request to a different domain.
