I've just tried to reinstall the Linux version of FTL, and despite the only available download language being English, the current download from the GOG website, 1.6.12 (2) is installing an Italian language version of the game, with no visible way of changing the language to English. Am I missing something really obvious?

Well, I found the solution in case anyone else has the same problem.
I needed to go edit ~/.local/share/FasterThanLight/ and edit settings.ini, changing the line language=it to language=en
Still not quite sure why it installed with Italian as the default though...