Like many others who have already posted here, and like many, many others you will find out in the wilds of the world and the Internet, I too have a story of being raised religiously (Catholic, even considering the priesthood in my youth), only to awaken to a greater reality. Realizing that I was an atheist enabled me to finally see the universe in "full color", and I have never looked back.
I do feel for you, but there are some hard questions you will need to confront:
If you hide you awakened mind, what will this mean for you? Would you be willing to suppress this, especially now that your are keenly aware that this is your only shot at life? If you were to reveal your true nature and be rejected, what would be your recourse? With your new vision, can you go back (what does that even mean now)? If your loved ones think you are simply going crazy or "losing it" how will you react? Would it be better to be "open" and suffer than to be "hidden" and choose self-censorship and repression?
Are your loved ones up for the adventure that you now see before you, unclouded by the illusion of the divine? Honestly, your now opened mind has available to it a universe that is terrifyingly beautiful compared to the prescriptive visions of a supernaturally-infused worldview. Sharing in this with other rationalists, especially loved ones, is sublimely wonderful: you are no longer in the privileged position of merely "observing" the trials and tribulations of this world as you pass from nothingness into eternal life here-after, but you really become a part of it in a way that the lie of religion cannot compete with. Although your are most certainly not alone in your dilemma as many others will tell you, it will feel as if you are alone a lot of the time in dealing with this transformation in your life, are you ready for it? Even if you are not ready for it, what are the alternatives?
The only "advice" I can offer is to be open with your views, but also make it clear that a rationalists view of the universe is not a negotiable point. In the sense that science, reason, and skeptical inquiry feed the mind of a rationalist; one cannot be asked to "please believe in God, for 'me'?" - such options are not on the table. They're not on the table because it is a request to substitute belief in fantasy in lieu of reality with no evidence to support such a belief. Be honest, be true.
Assuming that we evolved in the moral climate that you are constructing I would guess that we would readily kill babies. Now of course, in the example you give there is an inherent limit to the number of babies that can be killed and still have sufficient life left over to be around to respond to your questions.
The spectrum of responses and moralities I've seen on display here (and elsewhere) are artifacts of our being and culture. Many of the behavioral tendencies that we ascribe as being "moral" have both an innate ("instinctual" for lack of a better term) and a social/cultural element (i.e. learned or amplified). The idea of an "embedded" morality in the universe is a bit hard to swallow, but I'll play along: I would guess then, since we are also embedded in this experiment we (or any entity capable of expressing what can be judged as "moral" behavior) would eventually express this embedded moral behavior. It would be a rather fascinating argument to justify otherwise, given the "universe" as described has as part of it's makeup a particular moral code it would be reasonable to conclude that "moral" creatures would come into existence that continue to show a arbitrary collection of moral behaviors despite there being a supposed "embedded" moral compass? Then what is the meaning of such an embedded property if it not to be expressed? In the experiment as proposed the embedded moral direction is either relevant and expressed, or irrelevant and has no baring on the moral development of such a universe's inhabitants.
The general sentiment expressed about humans possessing morality is really a statement about some evolved behaviors that were selected, the rest (higher-level elaboration on these somewhat "innate" traits) is substantially illusionary. This is not to say that the more "illusionary" extrapolations aren't an important variable in societies, they are, but beyond the physiological and neurological elements, the rest are behaviors culturally and socially tuned to essentially arbitrary values.