Neil,
No you don't need to change your wifes Filipino passport. My wife travelled here (UK) on her passport under her maiden name. CFO is a mandatory seminar that your wife must attend before leaving the country. It can be taken either in Manila or Cebu. Following attendance of the CFO your wife will receive a sticker in her passport. She requires this to leave the Philippines.
You can change her passport in the UK. My wife has not changed hers and it hasn't caused any problems at all. If her passport is about to expire then it may be worthwhile doing now, otherwise I would leave it and address it when you have more important things sorted out such as the VISA and CFO.
Hope this helps
Steve