He also told me that I only need to say that the en suite was there before I bought the house and if I want to sell that I can buy indemnity insurance.
So he's encouraging you to lie? 
This suggests that he has done this kind of things many times before as he knew about all the requirements and how you can dodge the system.
He will only be able to 'dodge the system' as you put it, as long as people like you enable him to do so.
I am not sure what is the most sensible course of action as somebody on DIY forum told me that the council cannot remove the structure if it's been for two years.
You are still not listening. Nobody can make you remove it. It doesn't require planning permission. It should however be of standard that meets building regulations. That ensures that it is safe.
It's really very simple.
Get a comptent electrician to state what needs to be done.
Get the work done.
Apply retrospectively to the council for building regs sign off.
Expense should not come into it - you need it signed off if you ever want to sell the house. Indemnity is not appropriate in this case. You also need it sihned off to ensure it's safe. You'd be in a whole lot of trouble if someone was injured because of this installation.
Report the cowboy to Trading Standards. What he did may well be illegal - have you seen his qualifications. He could leave his next piece of work in an unsafe state.