Also, in addition to the extra diode Hero999 recommended, if the boosted supply is ever heavily loaded, and the input 13V supply gets disconnected, you'll need another Schottky diode from 0V to the MCU output.
Its fairly abusive to drive a large flying capacitor in a charge pump directly from a MCU pin, and if you don't add a series resistor, its likely to exceed the pin's Abs. Max. current limits. With a series resistor to tame it, and Schottky clamps, however, its reasonably robust. Unfortunately the series resistor to the flying capacitor increases the output impedance of the boosted supply.
If the flying capacitor is small enough, the pin's current limits cant be exceeded for very long, and in combination with the output's internal resistance, it may be able to survive the transient without damage. That's operating outside the MCU datasheet limits so you'll either have to do a lot of testing to qualify the part for this abuse, or discuss transient limits with the manufacturer's F.A.E.
Plot the current through the Schottky diodes and the source driving the pump to see why they are needed.
If you need to regulate the boosted rail, its possible do so in software by reading it with a potential divider to a MCU ADC input, and varying the PWM frequency accordingly (slower=less output), while maintaining approx 50% duty cycle. Its also possible to regulate in hardware if the MCU's PWM peripheral supports auto-shutdown and auto-restart: Use a comparator to detect if the voltage is over your desired threshold and if so, force the PWM to shutdown.