B&N has just announced a new updated version of the Windows 8 app they released in November 2012. Readers can now use their MS account to create a new account (via the Windows 8 app) in the Nook Store and use their existing payment info to buy ebooks.
What's even more important is that everyone who does not have the Windows 8 app can still choose to use their existing Microsoft account (with attached credit card) to buy Nook ebooks from B&N.
According to the B&N store-level folks I know, this feature first showed up over the weekend. It is in fact available to anyone and everyone who has an account in the Nook Store and doesn't actually depend on the Nook Windows 8 app. I just tested it myself, and even though I'm not running Windows 8 I was still able to authenticate the account.
You can add an MS Account to your Nook Store account by going to the B&N website, logging in, and changing your payment options. You can probably also do this from inside the Windows 8 app if you prefer.