driving a control pin to ground with different voltages
Yes, you can connect the EN pin to ground through a transistor, and control the transistor with the microcontroller. You are correct, the 100k resistor prevents a short circuit and the current will be quite low, so it will not damage anything. 

You may use an NPN BJT or an N-Channel Enhancement mode MOSFET, assuming you are using a positive voltage to do the switching. If you wanted to use a negative voltage (which you probably wouldn't since you're using a uC), then you would want to use a PNP or P-channel Enhancement mode MOSFET.

As already mentioned, since the enable threshhold rising-edge voltage only has to be 1.8v, and the disable falling-edge voltage has to be a maximum of 0.4v, then you can control it directly with your microcontroller, but make sure you don't forget the pull-up (which you already have). If you left it floating, it could cause some funky behavior and possibly even damage your circuitry.

I realize I am not the first person to answer your question, so only accept my answer if the others who already posted comments don't re-post as answers.