It sounds to me like you're being pretty strong and supportive about this.
I do think you're right to be upset/worried about the lying. Try to get to the bottom of that with her - why she did what she did, and hid what she hid.... If you can help her figure out WHY she was deceitful, maybe you guys can better understand what needs to change. Did she feel like being honest would hurt you? Or that bad things would happen if she told you? Maybe she feels insecure about being openly honest. Was she -afraid- to tell you she wanted to sleep with him, perhaps because you wouldn't "let" her? Maybe she needs to know that when she tells you something she thinks you won't like, or asks for something she thinks you won't give, that there will be constructive discussion.
As to how to help her feel better about this....
First, I think getting to the bottom of the "why she lied" thing is most important in helping her feel better, too. Once that is understood and addressed, a lot of the guilt can be better placed and dealt with.
Second, having sex doesn't make her a whore. If you guys have an agreement that she can have sex with her boyfriend, then she's not doing ANYTHING "wrong" (again - work out the lying, because that _IS_ wrong). If you can find a poly-friendly, sex-positive counselor to help her work through this a bit, it might be a good idea. Our whole society is so disgustingly bent on making sex "dirty" for a girl that getting past that stigma is real and hard work. It's important for HER to get past that, whether she ever sleeps with her boyfriend again or not.
Next, just keep doing what you're doing. You sound pretty level-headed about this (asking her not to break up with the boyfriend until she's more grounded, giving her hugs, being calm, etc.), so keep that up. Be honest with her and love her; she needs it.
Lastly, make sure you're not forsaking your own feelings over the lying just because she's distraught about having done it. She DID wrong you, by lying. And now you're reassuring her about her wronging you. This could become an unhealthy spot for you, if you're neglecting any feelings of your own about it. If you DO have some hurt that needs to be addressed, make sure it does. That *may* need to wait until your wife is more grounded and stable, if possible. Or there might not even be any hurt there, for all I know. I'm not you, so.... I know nothing
Oh, and don't forget to give yourself a pat on the back for being so loving