He probably feels bad and is worried for the bottom. I mean, he knows his employer is toxic when it comes to relationships, he is watching this newer obsessive side of his employer blossom, watched the bottoms father get mutilated basically, and he is watching how the Top is essentially manipulating the Bottoms entire life at this point. And he is having to lie about all of that to someone he genuinely respects, emphasizes with, and sees as a good person. He probably knows this is gonna blow up and the one who is gonna hurt the most it the bottom.

Why is Mr secretary looking at him like that?