Stuartfarm, as said by others, you can do it later. The only problem is that doing it from abroad is expensive (IE 140€ for changing the passport at the Philippines Embassy in Paris, around P2000 in the Philippines if I remember well).
Another thing, to avoid difficulties at immigration it's important to keep the same passport from the visa application till the arrival in the UK. Same name should appear on all papers (passport, visa, tickets). It eases boarding and immigration at departure and arrival.
So if your wife have time before to wait the recording at NSO to get the NSO sepca marriage certificate (required by DFA for the change of name on the passport) and the leadtime (I would say 2 months to be sure) to get the new passport before starting the visa application process then go for it. If not, she have to keep her actual passport... if its validity is sufficient (I would really suggest a minimum validity of 1 or 2 years). For travels, usually the validity should be 6 months over the visa validity and return travel date (if applicable of course).
