I still don't quite believe this but the documentation for 1.0 sounds like the pullups are *not* active for pinMode(INPUT).
They are not active by default. They can be activated, using digitalWrite(). Or, the call to digitalWrite() is made for you if you use the type INPUT_PULLUP.
I think that the "disabled" in that sentence refers to the fact that there is now a call to digitalWrite() in the pinMode() function. It is called with HIGH or LOW based on the use of INPUT_PULLUP vs. INPUT.
A peak at the code confirms this. The digitalWrite() function isn't actually called, but the equivalent register manipulations occur.