Hi Tone, firstly let me say I'm so very sorry to learn about this.
I do hope your MP will be able to find a way to secure a refund.
You made an 'honest' mistake and I personally feel you should get one.
I cannot stress enough the importance of following all the UKBA rules whenever dealing with them.
There are many postings here in the forum about ILR eligibility such as
this one here posted just a couple of weeks ago.
In the quote you use in you post I have highlighted the key part:-
Here's what UKBA state about applying for ILR under form SET(M):-
Michael, as I understand it your wife entered UK as a spouse? In which case the eligibility for ILR is 24 months living in UK as spouse. Application can be made 28 days before the 24 month anniversary.
As long as you comply with the rules you'll have no issues.