If all the films are canon, I'm now saying it definitely had to have been the droid.
Look at Prometheus and A:C. The movies show that androids are pure evil.
Why should Bishop have been the only non-evil android?
Why would Bishop go beyond following the company's orders? We all know the company wanted the alien. Bishop would be programmed to follow the company's orders. And he did not *directly* harm any people, just as he said he wouldn't.
I know there are still problems in this theory, but I do think it makes a lot more sense, even if traditional lovers of 'Aliens' don't like it.