You should read the documentation of the controller. Some pins may be 5v tolerant, but may be or not be in ADC mode.
Next, you should think about how much accuracy you need. If you use a low voltage linear regulator to get 3.3v then I guess you could use the ADC with the Vin as voltage reference. But you may want to consider using the internal voltage reference configured to 2.048v or 2.5v. With 2.048v voltage reference, you'd basically have 50mV steps and a division by 5 using the voltage divider giving you 0-10.25v measurement ability, and you'd still have the range between 2.048 and 3.3v as over voltage protection ( 3.3v x 5 = 16.5v)
Zener diodes would probably be the simplest method to add some protection. Something more complex I thought of would be using a schmitt trigger in combination with a p-channel mosfet. Give the schmitt trigger the voltage through a voltage divider and configure it in such a way as to go high when voltage goes over 10.5v and low when voltage goes below 10v (or something like that). When output is high , the p-channel mosfet breaks the connection to the adc.
Something like this is used by various overvoltage/undervoltage controllers, just google for "overvoltage p-channel mosfet" and you'll see various integrated ICs using p-channel mosfets to protect stuff.