Hey snman31,
I'll qualify this post by saying that my wife and I did a week long charter in the bvis for our honeymoon and it was complete MAGIC! We went off season and had it all to ourselves. Like you, my wife had only been sailing a couple years, mostly just on my little hobie 16 and some weekend charters in San Diego, and loves sailing. A couple notes: I haven't sailed the Med, but unlike the BVI's, where all you have to do is pick a mooring or drop the hook, you will be required to med moor, which can be tough. If she is a legit deckhand, and you are pretty good in reverse, go for it, otherwise, practice and then go for it. Also, I'd recommend finding a spot with pretty short passages. From my research, it seems that there are a lot of passages in the greek islands around 10 - 15 - 20 nms. They are great for the skipper, but can be a slog, particularly when you want to be sipping cocktails and enjoying new anchorages. A bunch of 5-8 mile passages and one longer one is perfect. So I guess my advice would be to be prepared. If your wife is able to help pick a mooring, drop
anchor, med moor, throw in a reef (re: meltemi) and steer (something could happen to you), than go for it, just be real about handling the boat.
I will say, that a cruising honeymoon can be incredible. It will bring out the team in you and your wife, you'll have some solitary moments that are undescribable, and sailing is just awesome.
Steer away from the flotilla's, they won't help you from the need to have the skills mentioned above, they'll just crowd your every stop. The charter company will help you plot a great route. Speaking of which, I HIGHLY recommend the Moorings. They may be a bit pricey, but they're the best.
Have fun and go for it!