Well, if he had two heads, sure, but he doesn't. Since it's just the one head, how would the one esophagus know which food goes into which stomach? No, I think the blended digestive system makes the most sense.

The real question is, which parts of the eagle's digestive system remain? I submit [url=http://digestivesystemsxavier.weebly.com/bald-eagle---haliaeetus-leucocephalus.html]this[/url] for your approval. Do griffins have crops or gizzards? They certainly don't have teeth, just a beak, so how much does that influence the digestive comparisons?

Perhaps they have a unique organ all their own, built to accommodate both varieties of diet. Something akin to the crop and gizzard that catches bony pieces and grinds them down, but also allows the easier-to-digest meat to continue through to the stomach at the same time?