Something doesn't add up to me; I can see corrosion causing a problem, but it certainly shouldn't cause problems to that extent; I wonder if he's having you?
The management systems between years will be similar, but the ball-ache is that if you have to buy a new ECU, everything will have to be replaced with it and the whole system re-programmed. FWIW, I'd try the immobiliser transceiver first (the sensor on your ignition switch) and try and clean up the corrosion; it'll still be expensive but when the alternative is scrapping or a £2k replacement system, it's probably worth a try. I paid £3500 for my '08 S2 (now at 12k miles without a problem, touch wood), and if a mechanic told me I needed to spend £2k to sort a problem like that I'd hand him the keys and buy a different bike.
How long have you had it for, and did you buy it new or used? Dealer or private?