This is not a specific situation, I just like to see Shaun becoming less antagonistic towards Desmond as the latter's character gets better and better.
Shaun is used to death, he began watching horror movies as a teen. He didn't really like them, all the blood and gore created by a mindless killer. He's read about death and murder in all his history books, seen them in documentaries and, after being recruited by Rebecca, has seen some Templars be killed. It was nothing fancy, no rite into the brotherhood, just a simple kill to get him where he needed to be.
Working with Assassin's did not change that. He's seen people of different shapes and sizes come through, all of them looking tough, cold and calculating. That's the last thing he'd want to say about Desmond, ex-bartender extraordinaire. The man could barely read the database when he was supposed to. While he had skill in the animus, Shaun couldn't believe that those skills could transfer to reality no matter how much it would benefit him. He always felt safe in the presence of assassin's, even if he didn't realize it, but being in Desmond's presence just pissed him off.
Then he saw Desmond practice his free-running skills with Lucy. Shaun had to admit, Desmond looked like the real thing as he scaled the walls of the facility they were in. He would never tell the assassin that much.
Next he saw him take on for guards at once. That changed everything. The goofball gunk-for-brains turned serious at the drop of a hat. His golden eyes became dark, his lips became a straight line and his body tense. Shaun watched him cross the room in three easy strides and feint the first guard, grabbing the baton that was swung at him and twist around to slam it in the second guard's face. Somehow, he dodged a bullet aimed for him and twisted around to stab that guard in the gut with his hidden blade. The last guard was taken down with a slash to the throat.
Covered in blood and still feeling the rush of the fight, Desmond had glanced around for his next victim. When he came up empty, his eyes flashed and he was regular Desmond again, a bit dazed and a quieter than usual, but he wasn't a danger to his team. Shaun didn't want to admit it, but he knew that Desmond was an assassin and would make an even greater one later.