ARM: Read the value of an Alternate Function pin
Apparently not, and I haven't seen a microcontroller that could. When you assign the alternate function to the pin the signal is rerouted to that function's interface, away from the GPIO register. If you assign for instance the I2C function to a pair of pins the microcontroller will say that what happens at the pins is none of your business; you'll have to pass at the I2C controller.

It's obvious that the pin can't be used for output, because of the conflicts it would cause, but while the use as input is more harmless it seems to be pointless, since the I2C controller will give you everything you need.  

Debugging is a possible purpose, but that's not the function of the microcontroller, that's what we have scopes and logic analyzers for.