Since we can't exactly apply actual physics, such as the laws of matter, I guess the best I can do to rationalize the clones was that they were made of magic. I think that if Twilight had struck the real pinkie pie, nothing would have happened as she herself isn't of magic, or at the very least, of a magic foreign to that of the pond, where they were being sent to. As posted on page 1, the Pinkie Pies were acting with emotion but... perhaps the pond only copies the most basic of a pony's personality? We know that they definitely do not copy the pony's intellect and experiences, otherwise they would have know all of the Mane 6's names.
When we come down to it, how would we define life? Would it be defined as being conscious of one's own existence? Animals of our world are, and obviously we are as well. However, as mentioned earlier, the Pinkies only showed one desire, to have fun. Nothing of anything else. Not even the most primal instincts that all living beings as we know it to possess.
tl;dr, In my opinion, the clones were magic, and without any primal instincts and consciousness of their own existence, makes them non-living. I believe the magic of the mirror pond was only being dispersed back.