We just got married this past June and spent a week at WDW for our Honeymoon. It was wonderful!! Such a great ending to our wedding plans!
As for the registry, GO FOR IT! We put around $1,500.00 worth of Disney activities on there (meals, outings, etc.) and got all of it. It paid for the parts of our honeymoon that we didn't pre-pay; we'd already paid for a meal at Cinderella's Royal Table, hotel, and park tickets. But, we felt so great to be able to eat anywhere and do anything that we wanted to do! Just don't rely completely on that for your spending money, though. We made sure we had everything ready to go as if we didn't get any of the honeymoon money the week before our wedding. The Disney money was actually what all of the last minute shoppers bought us; we had about $300.00 on our card the day before the wedding, and it was full when we called the morning after the wedding. We ended up just leaving the cash we had taken out of our own accounts at home since we didn't need it with the giftcard.
Just don't go overboard on adding activities if you do want gifts from another registry; we were completely newlyweds in the entire sense. I've been living on my own for nearly 5 years, but DH hadn't been. So, we needed pretty much everything home-wise to start our life together. If you go overboard on the Disney registry, you may get too much from that and not the things you were hoping to have when you get home from your honeymoon.
You can also add/subtract things as you go too; I know some people are hush-hush about checking their registries, but it's really the only way to keep up with items that may have been double purchased, etc. If you see people just buying your Disney money, then you can always take things off of it so they'll pay attention to your other registries. The Disney registry is much easier for people to fill out a form online than going to the store, sorting through a print-out, and searching for an item.