Next you'll be suggesting that video game characters should be able to just hop over knee high barricades!
Nah you're describing a different thing. Its not about realism. Internal inconsistencies are the issue. If in most of the game they can hop, but then can't for the last gameplay bit, and then can again, sure thats an issue. But suspension of disbelief of external things (like regenerating health) are not the issue. Not about "realism."
Its the fact that Soap uses his knife frequently in the gameplay melee attacks. There are unique dedicated melee finishers with his knife. The writers knew they needed to show Soap dropping his rifle to try to portray him as unarmed. But they apparently forgot or didn't care to bother actually disarming him. Either don't build the entire end game fight around the premise of the character being without any weapon - or - remember to remove the character's weapons from his body. (Ironically the entire climatic end battle of MW2 (2009) was built around Soap's knife.)
Everytime you break internal logic established within a story, you are effectively shaking a person who's asleep dreaming. The player is in the story mentally, but if you shake em too much they'll wake up and the dream is over. The illusion falls apart. Soap's knife magically appearing on him in the end was far from the first moment. It was just the funniest and most glaring example after many that had me so out of the moment that I was aware enough while playing to stop and capture the screens. Plenty of other stupid shit came and went shaking me from the experience a lil bit each time. Eventually it just piles up.
On a larger longer term scale this is what happened with game of thrones btw. Plenty of moments of dumb writing even in season 1, but audiences kept trying to enjoy the story anyways. But by season 8 it had become so frequent and had amounted to an unavoidable level of nonsense. So the last season was universally criticized as shit writing. rightfully so of course but it was far from the first season to suffer from lazy, dumb writing. It was just the straw that broke the camel's back.