I found it a little uncomfortable to watch, but it totally made sense to me. Intimate friendship isn't always comfortable, and sometimes when one friend is really hurting, the other just has to be there and take the backlash. It's Merlin's personality to poke at Arthur and it's Arthur's personality to repress until it bursts out.

I thought of it as Merlin performing an emotional medical procedure. Lancing the wound, so to speak (no Lancelot pun intended there).