jonathang:
Question for you as a lawyer.
If the call centre had argued that the flights were valid.
You booked to get from A to B and then B back to A.
The fact you required X number of hours at B was not part of the contract.
When booking you agreed to their Terms and Conditions.
How would you fight that ?
It would go something like this: Although you say that you're a point-to-point airline assuming no responsibilities for onward flights, connections or transfers, there is a difference between a journey from A to B using transfers, and return/round-trip travel A->B->A. You specifically sell round-trip travel, and such a round trip is booked all at once on the same PNR. It isn't booked as two one-way trips. That's a specific decision which you have made; you could have taken your one-way tickets-only policy to extremes by never selling round-trip travel as such.
If you sell round-trip travel, you know that the only way that the pax is getting to B to start the second sector, B->A, is by flying on the first sector A->B. It is therefore implicit in a round-trip ticket that B->A will follow A->B. Nothing in the terms and conditions prevents that being implicit in the ticket; the ambiguous language about "onward flights", "connections" and "transfers" will be read by the court in the pax's favour and against you, to refer only to excluding your liability for missed connections in the course of travel from A->B involving transfers. This is in accordance with well-established principles of legal interpretation, because this is an attempt by you to limit your liability.
Therefore, as it's implicit in the ticket that B->A will follow A->B, you must accept responsibility for ensuring that the pax can make a round trip A->B->A, or else you must remedy the fact that he holds a useless ticket. You actually acknowledge that yourself, because your website imposes a compulsory minimum stay of 90 minutes between the A->B and B->A sectors when you book a round-trip.
Furthermore, if contrary to the above you do establish that your terms and conditions mean that you can sell a round-trip ticket, then delay the pax on the A->B sector so much that he misses the second B->A sector, but still have no liability to him for the second sector because he has missed that flight through the first sector being delayed, then the exclusion of liability is an unfair contract term and the Unfair Contract Terms Act 1977 will render the term ineffective.
("You" obviously means FR, not jonathang!)
As I can do that off the top of my head without looking at any books, just imagine what a fight FR would have had if I had really had to get stuck into the problem.