I recall reading that it was Roy's personal composition and that he hadn't actually wanted to perform it until Ronnie asked him to, but I've forgotten where that was from.

Anyway, the Corries were always pro-independence, and they obviously did a lot of the '45 songs- those are almost always anti English (but they are very, very catchy, just look at "Killiecrankie"). Ronnie was in an interview saying that Roy had been trying to antiquate the Flower of Scotland melody to make it sound more like their usual Jacobite repertoire, so if the lyrics were also very Jacobite-ish- aka anti-English- it's not actually surprising. Perhaps Roy half-accidentally-intended to make it anti English? He wanted the song to sound folkish, after all.