Read Switch Status without interfering with LED
Your second circuit is perfect, provided that the pullup on the input is enabled. 

When the switch is open, the anode of D1 is at VDD, and the cathode of D1 is at 13V-Vf. The diode prevents the higher voltage from reaching the input pin and destroying the MCU.

When the switch is closed, the cathode of D1 is at 0V, pulling the anode down to 0.7V and registering a low at the input.

You don't need the resistor since the pullup will not source enough current to damage the diode, but you must have the diode in order to prevent the higher voltage from reaching the MCU.