You pay your money, your take your chances!!!
Yes this route is pushing the A320 in a charter config. A 757 is much more suited on these particular days, but uses much more fuel/costs on all the other days!! !!
It is most certainly fixed cost, so Air Malta will take the hit. At least they don't leave some bags behind and go non-stop like some other Airlines would!!
In general neither the ticket sellers nor the Airline give one hoot to the bucket and spade brigade so they wouldn't really care about any complaints as long as they have their money in the bank!
Flying time is different to scheduled block to block time. As flying time doesn't take into account taxiing time at either end, usually about an additional 30 mins total, so you were not time "scammed" by a corrupt ticket seller.
It could be a non-stop flight if the winds were favourable just like on the way down, but unlikely with the prevailing westerly winds over Europe , as the Captain attested!!!!