"Aubrey was a very complex man, full of contradictions, his unquestionable sense of duty, combined with the fact that at any time he could have been found guilty of treason for permitting a catholic to serve onboard his ship as ship's surgeon"

The penalty suggested sounds abit more than discrimination Charley. In time of war particularly around that era I don't think that the navy were too choosey about where they got their men - a quick look at the different nationalities onboard "Victory" at Trafalgar shows that. The Catholic Relief Act of 1778 was introduced for one reason, to allow catholics to enlist without having to swear allegiance with ties to the Church of England. Our American friends might notice the significance of the date, which might explain why the British needed people under the colours.