The "phone call" was John's plan, but just talking to Rilye's foster Dad. Talking to John was Cam's idea. It seems to me, especially after last weeks ep, she does indeed have very real deep emotional feelings for John. When she came to him earlier I don't think her motivation was to proclaim her innocence in Rilye's death but more to try to "comfort" him in his time of need. She said she was sorry for his loss. I think she thought (in her own way, totally ignorant of proper social ways) that hearing Riley's voice would comfort him (Why else keep imitating Riley's voice when Foster Dad couldn't hear it?). The first thing she said was "I thought you'd like to hear my (Riley's) voice" The "I love you" part, was in my opinion, an "opportunity" for her to express her real feelings toward him in a way she thought would be "safe". I think this is something she has been wanting to express for some time but afraid to, as she new it would probably just serve to "alienate" him from her. When she did say it, there seemed to be a bit of hesitation there like she was building up the courage to say it. When he was walking away from her after the meeting with Foster Dad she said "you shouldn't be alone" with a bit of emotion in her voice like she was very concerned for him in his present mental state.
How does John feel toward her? well like you said he likes to hide his feelings, but there is plenty of evidence that deep down the feeling may be mutual. He always comes to her defence when she is accused of something, even lies to protect her. Something else to consider is that no matter how "human" she may become, the fact is that she is a Cyborg and always will be. If he does have, and I think he might, deep down real love for her, I'm sure it would be hard for him to accept, causing him to try to repress it as best he can. Sarah can see this I think better than he can (his feelings toward Cameron) and is probably at least 50% of the reason she looks at her with total contempt and considers her a threat to him.
Some insightful comments by sNaKeBiT and Sahlinrob- at first I just thought Cameron was being particularly inept in dealing with humans when she got on the phone with John but the more I look at it it does seem like she is using the moment to express here true feelings towards John. I remember the obvious longing in Cameron's eyes as she watched John and Riley at the very beginning of "Mr. Ferguson is Ill Today". I think too that when Riley tells Cameron,"Get it through your head, you're just John's sister." she's picking up on Cameron's suppressed love for John.
As far as Cameron always being a Cyborg? Well I have high hopes of the Good Fairy interceding and turning Cameron into a 'real live girl'. Then again who's to say that John and Cameron won't end up settling down together and raising some mechanical kids? World War II didn't end because every last Nazi and Japanese fascist was hunted down and killed but by the slow democratization of the former enemies. Could a similar scenario be possible with machines in the future?