For your safety, you should assume that everything you put into the service is public.
Our intent is as follows:
At this time, we don't plan to publish your scripts or the output (except for the aforementioned caching).
As this is a beta service, it's possible that there are security problems which will later reveal your scripts to attackers. We're working hard to ensure that your data is private, but we're not perfect, and part of the free nature of this service is that you're sharing resources with other people. This makes security much, much harder.
We intend to provide a paid service later. Part of what you'll get in return for paying for the service is that we can provide much stronger security and hence stronger guarantees around the privacy of your data. For a free service, it isn't viable (from a performance or a financial standpoint) to provide that level of security.
So while we have the best of intentions, we can't promise anything, and we do want to use metadata from your scripts to improve the service and provide better security to the R ecosystem in the long term.