Nice link, WebyJ!
To the OP: I'm not Vicky, but I can point out that the granting of ILR on the basis of marriage to a UK sponsor only works if the applicant was not in breach during the probationary period, and not in breach at the time of application. On the first of these, you're ok. On the second, you're in breach because you applied for ILR without unspent leave.
That means you don't qualify under the rules. It also means your employer stands to be done for up to GBP 10,000 unless they can dig up a statutory excuse.
Illegal. Like it says in the link WebyJ provided, they have withdrawn the DP3/96 provision and replaced it with Article 8. So they are not going to deport you or break up your family etc etc. And if anybody tells you differently please identify them to me in PM so I can turn them in to the regulator for exploitation.
What will happen is that UKBA will make a determination on your app. Given a fair wind, they will grant a term of FLR in which you can get your act together and regularise. My guess is that you might have to extend FLR even again after that, but that's just a guess.
You can very well expect your employer to get a ringy from the enforcement unit also.
