Have you looked at restoring the master secret? http://msdn.microsoft.com/en-us/library/ms942583.aspx. There has got to be some way to reuse the existing SSO database.
By the way, is the SSO master secret is running on one of the BizTalk servers? If you run the master secret on a separate cluster (like SQL), you will be better protected. The master secret really does need to be clustered because it is a single point of failure for all of BizTalk. However, you usually don’t want to cluster it on your BizTalk servers because doing so would force one of your BizTalk servers to be passive.