STM32 Protection Diodes and Voltage over VDD
My question is does anybody know the forward drop on these protection diodes?


Read the datasheet carefully. The absolute maximum ist usually stated as VCC+X - the X is the forward drop of the diode.


  [...] soltuion to this problem.


Switch the LED supply off at the same time, using 2 FETs. Alternatively you could use a N-channel FET to switch each LED.