Have you got the NSO copy? The NSO copy is authenticated and does not lose it's validity. Thats the one you need in your spouse visa application.
The Marriage Certificate does not need to be authenticated by the DFA. You will need to take the Marriage Certificate to the DFA if you wanted to change your wife's passport details to new married name but you don't need to do that for the spouse visa application. She can apply using passport with her maiden name.
You will also need the NSO copy for the CFO meeting which she needs to go to, this can be done before or after applying for the spouse visa.