My naive argument would be based on energy conservation. I won't write any equations. This is for you to do.
The bike + rider has both rotational and translational kinetic energy in addition to the potential energy of the system. When you apply the brakes, the translational KE is converted to both rotational KE and PE which manifests as work done against gravity. You lift up, pivoting about a point, which accounts for a change in rotational motion due to an external torque (friction).
A very interesting real world experiment which I do every day (I bike to work) is to stand up if I wish to brake efficiently (in my case it is only marginally efficient, but I do feel the difference). The translational KE is converted to PE and hence the brakes don't have to work as hard to stop my motion. The heavier the person, the more effective the technique.
So, if you are a fat bastard, this may be a useful way to stop quickly.