Hi ramsay - A lot of us have faced issues with middle/maiden name when applying for UK passport. However, I think your problem is probably easier to resolve. Since your wife has no valid passport/travel document with the maiden name, you may find it easier to get a British passport with the 'new' name.
1) You will need to contact Home Office ASAP (
Citizenship.support@gsi.gov.uk ) to get your name changed in certificate (before ceremony). They may or may not charge you a £162 fee. In your case, you should fight for a FREE change as you had mentioned on your application form but they did not comply. You may be required to send along a deed poll as proof of name change from maiden to married name. If you do not get name changed on certificate, the registrar at ceremony cannot help you.
2) If you are luck with your HMPO case worker, you may be able to skip step 1 and apply for UK passport with 'new' name. In my case, I was able to get British passport without changing name on certificate. I sent a deed poll (made it myself) and sent to HMPO along with GOV.UK print out. See:
https://www.gov.uk/changing-passport-in ... -documents
In any case, you may find it easier to go with maiden name. But if you are really fussed about changing name, do it now rather than at a later stage. All the best.
