Again, the punishment is limiting resources that cloud appear on the CS quest or WLTKD. This is why you sometimes not want a resource. To avoid this negative aspect of having a resource.But you are not getting punished. There is a difference here between the two things that is somehow lost on you. If you build a building, such as the library, you get a passive reward so to speak -- the +2 science income, the specialist slot, unlocks of another building (the university) etc. So you get a reward from here on until the end of the game for having built that building. If you improve a luxury or a strategic resource on the map you get a reward in that resource, you get something you can trade and the plot usually increases by a few points in some yield. Those are rewards. You did something and now you get rewarded.
If you complete a quest you get a reward for having done something, it's a one time payout and then it's done until you finish the next quest. They are not supposed to be retroactive. You have done something here and now and here is your reward for doing that. They want that wonder, luxury, strategic resource NOW and they'll reward you for it. Not that you have ever built it or done it sometime in the past.
This is the thing, in game as in reality -- People want new things! Things that they do not currently have. This shouldn't be an alien concept.
But for some reason that I think is still somewhat unclear you can't explain how completing a quest in an exploit. Not to mention that you are somehow fine, or want, to get rewarded for things you have already done even tho said action you took have already been rewarded by the game. So you want double rewards for something already done? That isn't exploitative and gamey? Is the exploit that you chose to wait hoping for a better reward at a later time? If that is the case then you shouldn't even have an option, the AI should just say "Here have some luxury and you are going to like it and you can't refuse!". On top of that by turning down their gifts or letting the city-state quest stay there for a bit before I try to complete it I'm not getting any reward. I'm getting nothing. I run the risk of the quest going away, there could be a war and for some quest someone else could beat me to the goal. If I turn down the gift I don't get anything, I get a diplomatic penalty on top of that for refusing their gift. Then there is the added risk of when I actually want the luxury (or whatever) it's not available anymore; perhaps the AI gave it to someone else or now they hate me for turning down their offer.
If you can't trigger a WLTKD within a reasonable amount of turns you are doing something wrong.
I've never said that completing a CS quest is an exploit, so please don't twist my words. I said that avoiding requiring a resource just to get easier quests is unnatural, gamey and probably alien concept to AI that could give advantage to the player. Hence I call that exploit.