Transient and reverse current
It sounds like you are trying to make a digital to analog converter driving some type of load.  Look at this link: http://emesystems.com/BS2PWM.htm
It will give you a start. Please note they use an opamp as a buffer.  

This 'buffer' has a very high input impedance and a low output impedance.  It can drive from a few mills to over an amp depending on the opamp chosen.  Additional circuitry can get you into thousands of amps if desired.  The schematic is a 2 pole filter originally designed for the Stamp microcontroller. 

The filter soothes it out but adds a delay on the final output value (settling time).  The greater the filter capactance the lower the ripple and the slower the response.  You can add another pole to filter if you want.

As a bit of information from an old semiconductor guy absolute ratings are just that.  If you exceed them even for a few nanoseconds you can be sure you damaged the device, you just do not know when it will fail.

I have seen a lot of microcontrollers damaged because of capacitors connected to the pins, power excluded, doesn't matter if the pin is input or output.  When the power supply collapses it will inject current into the microprocessor substrate possibly damaging it.

Good Luck