Manufacturer offer to clean it? Hmm.. Or is it the shop who offered to clean it? To my knowledge, if you get access directly to the manufactuer, they would usually have the lens changed and disposed off the lens. For parallel import shop owners, they'll do "cleaning" themselves..
Anyway, have the lens changed. Once fungus grow on the lens, there is chances that the cleaning process may remove some of the multi-coating on the lens. And if done inproperly, there will be uneven coating on the lens. If you know about multi-coating sputtering, then you would want to have it exchanged for a new one.
Aiya, for sleeping peacefully at night and the thought of getting your money worth, ask for a new lens.