I say bring it up. Definitely say something to him, and maybe if its a super big problem, I would hope he'd say something to her.
I'm kinda on the opposite end of your situation. One of the guys that I used to fool around with a lot and had a super huge crush on recently started dating this girl. Dude is also one of my bestest friends ever. Seriously. My roommates have been informed that if ever anything happens to me, they are to contact him first. He is really smart and a really great guy and I trust him with my life.
A bit before he and his lady started dating, we had sort of stopped communicating. We were both just busy and didn't have time for each other, and we sort of got into an arguement about it. I didn't find out about the lady until they were pretty serious, and I was kind of hurt by that. And it was due to us not talking. So I vowed to keep in touch with him more often.
Well, his lady makes him awesomely happy, and that in turn makes me happy, so I really really enjoy talking with him now. On top of that, a bunch of shit went down in my life, and since I basically cannot trust my family, and a lot of it involved them, I turned to him. He has been super helpful, and I probably would not be here if it weren't for him.
Admittedly, I always feel bad when I call, because I am worried that they are spending time together, or that I will interupt them. Twice I've called and I could hear his lady in the background and I felt bad. I don't want to put a strain on their relationship, you know? I really want them to work out. Dude totally deserves it. Plus I love hearing him when he is happy. Its pretty much the greatest thing in the world.
But yeah. If I was making her uncomfortable, or if our talks do make her uncomfortable, I'd more than apperciate her saying something to one of us. I mean, either just her calling me up and saying "hey, I know you two are close but it kind of makes me a bit uncomfortable" or her saying something to him and him saying something to me. It'd be apperciated.
tl;dr: Emaline is a sappy sappy fool. Prefers when her friends are happy, and would want their girlfriends to be all "he's mine, bitch!"