Hmm... I've had time to marinate with the issue for a couple of days now, and toy with a few ideas I had.
Towards the end of the conversation, (just before Nick arrived with his army of H.E.R.B.I.E's-on-'roids,) I think Richard knew the jig was up and almost told Peter what he wanted to know. Taking just those few words, one can infer a lot.
"Keep in mind, you were never supposed to see her..." I'm paraphrasing here, of course, but even if he managed to nab Gwen's corpse and reanimate her, it was only for convienience.(sp?) He may not have known what the result of the experimentation on her would have been, but afterwards he knew what he and the C.I.A. had on their hands - a genetic cocktail attack dog... a Hulk-Lite.
Gwen doesn't stay put, however. She escapes from wherever she is held, (lending to the belief hat she's really not aware of what she is doing as Carnage,) and goes to the first place she can think of. Her home. She lucked out Peter was there when he was, or I think she would have been picked up and shipped back to the lab. Chaos ensues, and enter Richard Parker, fully suited to the task of wrangling their no doubt expensive and valuable speciman in.
Should this particular theory pan out, (and I think it might,) Richard Parker's motives are no longer ambiguous, they veer straight into immorality. Sure, he was paid by the C.I.A. to develop such a thing, but appearing to his Son under the pretense of assisting him is simply horrible. Someone, (who I don't think is Richard,) is seriously screwing with Peter, and this will only add to the weight he is already struggling with. I think in the next issue Peter is going to have to protect Gwen/Carnage as much as battle her/it, and we just might get an idea of how big this whole conspiracy is.
Fury knows something.
Richard knows something.
And Peter will be too busy trying to save someone beyond saving.