"aux vaches"
Any professional pilot reading this would have their head in their hands.
It isn't a question of "common sense", the rules relating to who may or may not sit sit in the flight deck are from statutes empowering the DfT to issue mandatory instructions to all UK carriers and to those foreign carriers operating into and out of United Kingdom territory and airspace. The company had no discretion or authority to endorse or sanction any request that violated the law. What the Captain might have done in extremis, would no doubt be subsequently judged on its own merits, but you can be assured that any violation of this rule for purely routine maintenance items was a complete non starter.
Seats are not usually individual items, so if yours was not secured to the floor rails, presumably the entire row was insecure. If indeed this was the case, then no right minded Captain would sanction departing in such a condition. Even if the row was unoccupied, the potential danger of a loose major item of cabin equipment would normally preclude departing in that condition.
I am afraid it all sounds a little bit suspect, but if indeed the Captain sought permission to set aside the rules, and was denied that permission (as you would expect), then that is not a failing of the company managment, in fact quite the opposite, they complied as they were lawfully required to do! Your "obvious solution" wasn't in fact any solution at all. The Captain presumably knew that, otherwise he wouldn't have needed to seek further guidance. The company knew that as well.
Again, it is hard to imagine any Captain certifying the acceptance of a seat in an unsafe condition, and given the nature of these seat rows I am a little sceptical that he actually did, although I appreciate your interpretation of the situation, it may lack the full facts that were prevalant at the time. However you were there and I wasn't, so if what you say was the case, then this Captain would seem to have made some very poor and fundamentaly flawed decisions. Safety would be a paramount concern and any perception that your "expensive" holiday would be wrecked, or that statutory rules and regulations should be set aside to change that priority would be risible to any aircraft commander.