I realize I don't have the whole story, but since you and your wife seem to be on good terms at the moment, being engaged with her and discussing this stuff, and especially voicing your concerns, is still a good thing to do so long as you can do it in a reasonable, rational way, with control over how you express your emotions.
I am certainly no professional and have no business giving advice, but my W was in a 3 year R w/another man and we're still together, and doing pretty well, so I kind of identify with where you're at and hope you can avoid going through the kinds of things me and my family went through.
You should definitely consider all advice carefully. The things I'd recommend at your stage include the following:
1. Get into marriage counseling (both of you, together) as soon as you can with a counselor who believes his/her role is to help you strengthen your relationship and marriage. All counselors are not created equal. Find someone who's reasonably priced if your insurance or workplace doesn't cover it, but find the person who would be best for the job. It's worth giving up recreational money, eating sandwiches for lunch, etc., if you have to, believe me.
2. Tell her what bothers you, in a calm, respectful way. There's nothing wrong with asking her to stop. Not everyone may agree with me, but I don't think married people have any business pursuing or justifying a close friendship with members of the opposite sex. Period. It's disrespectful to the other spouse at the very least.
I recommend Michelle's books as well because they are so practical and helpful. There's a lot in there about detachment, getting a life, etc...in other words, making yourself a better, stronger individual...that is very good. Keep in mind, though, that the recommendations about avoiding relationship conversations and such really only apply if your W is openly rebelling against the marriage or is hostile. I mean, you SHOULD be communicating with your wife about how this bothers you. Again, HOW you do it is important.
It's tough because there's no way to know exactly what's going on...which is why she should be willing to cut off this kind of friendship completely. There's nothing at all wrong with you being uncomfortable with it.
There's no way for me to know what's going on in your wife's mind, of course. She may be telling you 100% of the truth. My experience obviously was different, so my perspective is permanently colored by that. Either way, since you two are even at this stage in your marriage, be ready and willing for some hard work ahead.
Best wishes.
You keep using that word. I do not think it means what you think it means. -- Inigo Montoya, 'The Princess Bride'