It is not unfair to give merits to whom you think it should be allocated. If you find a thread and you think that deserves merit, then instead of just giving a higher amount of merits to that single thread, I would suggest you check other threads of that user and analyze if he is really posting good contents on the forum or it's just one thread that he posted is good. By doing this, you will have clarity about the user's contribution to the forum and how much he deserves for that merit.

Also, if you feel if his other posts deserve merit, then you can distribute the merits among different posts.