Well, I don't think Shaw is literally raped by Holloway or anything, but it's clear something does violate her in some way, in classic Alien tradition.
Holloway can't be that visibly bad off first time out because as early as the first teaser, we see him in bed with Shaw onboard, presumably in the same sequence where he checks his eye. But he looks fairly normal there, as opposed to how he looks when we see them returning to Prometheus. Is that later, or did it 'clear up?'
