I read what you said and it seems like this.

She had a friend.

Maybe she didn't tell you because it seems like you might have blown it out of proportion...and she was right. you did.
Cool out, it is ok to have friends that are guys. If he made her feel better and less lonely well....isn't that what friends do? She wasn't replacing you, but she has feelings too and needed someone around to talk too. Why are you begrudging her that?
You are the one she goes too when she is lonely and needs a friend but you where gone and your relationship was changing. She needed another perspective, and maybe she felt guilty for it, because she wasn't talking to you; but she has a right to have feelings and friends. Get over your emotional stuff, and get her to communicate without fear, then ya'll will be good.
(not being scared to tell you things will help her feel like she can tell you anything)