I would really push to have it totalled. Any indication of it being a flood vehicle on Carfax will be the kiss of death for your resale value. I had a near impossible time selling my e46 because of two minor accidents on Carfax, never mind a flood indicator. I would expect somewhere around a 30-50% reduction of resale.
This needs to be argued with the insurance company and pay for a lawyer if need be. You don't want to take the depreciation hit, trust me.