So... My Sim is an elder and has an adopted child, which is a teen. Both father and son aspire Knowledge.
Some day, a matchmaker left a Lamp on my lot. One of the wishes my elder Sim made to the Genie was to be able to trick death. He basically died 4 times already and the Grim Reaper let him stay alive all these 4 times. Since he is dying of old age, he dies and Grim Reaper let's him stay alive every single day.

He was a cool Sim, but because of that, he's getting on my nerves. I could just delete him while Grim Reaper comes to take him, but I wanted to have his grave, and I am afraid he gets deleted as a whole, from the Genealogic Tree, the Memories, the game files.

Does anyone have a solution/an idea of what should I do?

You have to wait for his wish to run out.

Also do not delete sims! Not unless you want your hood to be toast. I do hope you have no unlink on delete? which is for corruption from deleted/vanishing gravestones.

It may take some time, but your sim's luck should eventually run out. Here's some info from the Sims Wiki about the "Cheat Death" wish:
http://sims.wikia.com/wiki/Genie

from my understanding, deaths where the Grim Reaper does not come would prevent sims from pleading for themselves. Cowplant is one; not sure if there are any others.
other deaths; I take maximum times for sim to plead for himself/herself is 10.