The only requirement that UKBA states in the supporting docs list is this:

Evidence of your marital status : This could include a marriage certificate, a civil partnership certificate, a divorce certificate or a death certificate

http://www.ukba.homeoffice.gov.uk/si...settlement.pdf
Now, what your wife has is the marriage certificate stamped by NSO. It is a legal document as they have stamped it already. All your wife has to do is try to get a marriage certificate that is copied on SECPA or security paper by NSO. If she can't get that by the time you plan to apply for a spouse visa, what you both currently have is still a legal document. UKBA won't refuse a visa just because it's not on security paper. They would inquire to NSO if you are really registered as married. PLUS, you can explain in your supporting letter about the details of your marriage cert.

Now, as what I've read in that link I gave you, it's easy to file a marriage cert in NSO and to get it copied on SECPA. Try it first so you know what your next step is.