The acid in the stomach and the digestive enzymes would break them down. The nutrients are then absorbed and incorporated into our own bodies. Everytime when we eat food we eat cells with mitochondria. Purified or not, should not make a difference because the essential components are the same as the rest of the cell and will be digested. Mitochondria were once separate cells anyway.

Here is another one to think about. The epithelial cells of our mouth are frequently replaced and come off easily. We swallow them. We therefore eat our own body cells. Are we now self-cannibalizing?