Never had the slightest problem with doing in the British when I found them (or anyone else) land or sea. I gathered from the story that Kenway is supposed to become a bit less of a bloodthirsty pirate as time wears on, but fortunately the game doesn't really force you into that. You just won't always get the full synchronization bonuses on some missions that have optional non-lethal objectives.
And perhaps it was just because I started doing the 'Kenway's Fleet' minigame as soon as I could, but I always had plenty of cash. I was blowing it on upgrading the hangout since the money was coming in much faster than the iron, and I didn't feel like going out of my way to farm for it.
Still, this was a great article about a great game. It actually encouraged me to go back and play the whole series (at more or less the same time), since while it appears to have little to do with the metaplot that's been built across the series, by the end it's revealed just how involved it's all been.