Rory had seen and heard and lived through a few unsettling things, disturbing things even, partly through his adventures with the Doctor, partly from his memories as the lone centurion. The timeline may have been erased and he may have closed the figurative door on the echos that remained in his own mind by the memories were there whether he acknowledged them or not.
As a nurse, Rory had some familiarity with Dissociative Identity Disorder although he'd never worked with a patient who had this condition. Niki's description so far made him suspect that was what was in play here. However, it wasn't like he could ignore the implication in her vague description. The men weren't 'just dead' but 'ripped apart' and there was the faint implication that she or some alternate personality was responsible for that. It was an uncomfortable possibility, especially if said alter asserted itself viewing him as a threat.
So, realizing he was a bit over his head but still committed to trying to help her and hear her out, Rory asked, "And how far did that go? How long were you experiencing black outs before you arrived?" Never mind the more disturbing question: had she blacked out since arriving in Red Oak?