The 1 NT bidder must accept the transfer, even with only 2 in the suit. Root and Pavlicek's book Modern Bidding Conventions 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 Jacobi 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 Jacobi 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.