In Standard American with strong 1NT openings (typically 15-17 or 16-18 points), the 1 NT bidder must accept the transfer, even with only 2 in the suit. Root and Pavlicek's book Modern Bidding Conventions (Standard American) is very clear about that.
This will not always lead to an optimal result, but like many other conventions, the first 2 bids of the JacobiJacoby Transfer are just the start of a longer communication sequence and departing from the sequence this early in the bidding would waste much of the benefit.
Also - despite the 5-2 fit, this is usually a good place for the contract to land when a weak responder is not even assured of taking a single trick (without ruffing). The contract with the 5-2 fit gives you a ruff or two from the dummy and an opportunity to attempt finesses that require a lead from dummy. In fact, I would go so far as to say that this is one of the major benefits of the JacobiJacoby Transfer, as a 1 NT contract with zero support from dummy often leads to going down 2-3 tricks, whereas the 2H or 2S contract with 5 in dummy and 2 in declarer can often be made.