So the question is who should compensate him for the extra 700 euros: the agent or the airline? I guess in any case it should be the agent- and they should claim it back from the airline if indeed they issued a valid ticket.
The OP is actually out the 1600E and 2300E, so at this point he's looking for a 2300E refund, not just 700E. But in any case, if the tickets issued were on valid fares that Skytours has contracted for with Austrian, Austrian should issue a refund for the new 2300E tickets. If Skytours was doing something shady, then they should be responsible. As long as Skytours is picking up the ball and running with it, then that says (to me, at least) that the Austrian personnel who made it their business to deny boarding because the fare was "too cheap" should have kept their noses out of it. My experience is that if the fare was invalid, Austrian would have eventually sent Skytours a bill for the difference after auditing the ticket, and the passengers would not be inconvenienced. Gate personnel have no business trying to be the rate desk.
As to whether Skytours should refund the passenger now, the problem is that eventually any refund issued will go back to the credit card. So if Skytours refunds the passenger now, and Austrian refunds later, the OP will have 2 refunds. What does Skytours do then?