I think you've well summarized the real issue.
Its fine if you don't like repair costs! Complain all day. Just don't say that your repair sink is greater than the gil fountain of all the combined players in the game. Its not true.
The 1000's of people doing leves/FATES daily far outweigh the small amount doing endgame. Yet those who run dungeons want the gil handed to them directly. If its not then they blame the economy.
You're right that there COULD be a problem everyone runs endgame and questing stops. But right now that is not the case and there is no proof or indication that it will happen anytime soon. Gil can infinitely be created by leves/FATES and there will continue to be new players for some time to come. Not only new players but people leveling new classes and doing leves/FATES/quests for each one.
What you describe is a far future problem.
