Hmm... so you want to keep processing payments during checkout and then hold onto some card data for processing the recurring fees? Is it possible for you to run the recurring fees through your gateway instead of storing the data locally? If not, can you get by with just the card number and expiration date?

There would be nothing stopping you from simply hooking into the order submit/save to store your own encrypted version of the CC details and using that information to process the recurring payments. The data is still a part of the order object during checkout.