Receiving a counterfeit item must happen so very rarely, considering the (millions?) huge volume of these sales per day, and Amazon is obviously swift to fix the issue (much to the chagrin of sellers swept up by the zero tolerance rule) that I really doubt most consumers would ever receive a counterfeit item in this way. It seems more likely that consumers would buy the "cheaper" option from an FBA seller (perhaps unknowingly) and receive a knock off.

The major logistical advantages outweigh the very low possibility of abuse. If you asked the average consumer if they would like to receive their item 2 days faster, but risk a 1 in 1000 chance that they get a bogus item they will need to exchange with Amazon at no cost, I think the former would win by a mile.