Just a quick update to this, I went to see my MP on Friday morning, think he was shocked to discover it cost £851 for a British citizen to get a visa for their spouse and nothing for someone from Europe. I think I had both him and his two assistants heads twisted with the complexity of it, he says he's never came across a similar situation in almost 20 years.
He was very helpful, I've dealt with him once before, genuinely good guy. Due to the timescales involved and the fact that my wife was supposed to travel this Friday night, he (or his assistant) directly phoned the private secretary to the Home Secretary to ask for reconsideration. They said they still required something in writing, so he drafted this letter for me.
He emailed the letter to me, which I forwarded to my wife, he's asked her to deliver it personally to the British embassy in Manila. I called them this morning, they tried to fob me off by saying go to the visa centre, when I explained that a Member of Parliament (now actually a secretary of state) had personally requested her to hand deliver it, they relented and said they would accept it.
By the time she got done with work today, she got caught in traffic and couldn't make it, so she's going to the embassy first thing in the morning to drop it off. Unfortunately the MP put the wrong dates in the letter for the times I worked, but I added a covering letter explaining this error.
Nothing to lose, so fingers crossed, hope we can get a result, otherwise I'll be starting the appeal process.