Why did my micro-controller short out even though the alligator clip of the oscilloscope was connected to a ground pin?
This is a dangerous-looking setup.  Connecting the ground clip of the scope probe to one of the GND pins was correct electrically, but a bad idea because stuff happens.

I think it's 80% likely that the ground clip swiveled around and touched the 5 V pin when you didn't notice.  This can happen very easily.  I wouldn't use a alligator clip on a pin like that for exactly this reason.  It is OK to use a "hook" clip, but be careful about them coming loose and popping off the pin and then hitting something else.

A possible option for your case is to clip to both GND pins together.  The alligator clip would come from the top of the picture, and only reach far enough to touch the two GND pins.  I still don't like that since it will pop off eventually, and then you've got a ground connection flailing around randomly shorting things.

What I use for these cases is a short wire that has a female pin meant for a RS-232 connector on one end and about &frac14; inch of bare wire on the other.  The whole thing is about 1&frac12; inches long.  The female connector has heat shrink tubing around it so that it is insulated on the outside.  Slide the female connector over the pin, then clip the scope probe ground to the short end of bare wire.