A paintball on bare skin feels about like a bee sting - but doesn't last like a bee sting. So realistically the only "vital area" available is the eye. Your plan is to hit a 1" target in confined quarters while under duress, with your life possibly depending on it?
Let's say you pull off the miracle shot. After all, if you spray enough rounds at his head your odds of success will go up, right? What is the aftermath of "stopping" the intruder? Well if I were going to break into a house, I'd probably do so armed. I would put the odds at 50/50 that the intruder, upon being blinded by an unknown substance, begins to indiscriminately fire handgun rounds in your general direction. Maybe he's using defensive rounds, hollow points that penetrate your walls less. But more likely, he bought a box of FMJ for $3 from whoever sold him a handgun with the serial number filed off - we're talking about a criminal, right?
So to recap: bad guy breaks in, bad guy gets paintballs to the face, bad guy panics and turns you, your loved ones, and your home into Swiss cheese.