Instead of having two English factions, it would make sense for there to be two Scottish factions, something like a Scottish 'Nobles' and a Scottish 'Rebels' faction - the rebels would always be at war with England, while the Nobles would either fight against the English, or fight against the Rebels. The names aren't perfect, since in real life the rebels also contained nobles, but it would more accurately represent the situation in Scotland, where the bulk of the nobility alternated between subserviance and rebellion. There wasn't any English civil war in this period that I know of, so it doesn't make a lot of sense to have two English factions that can fight each other. Of course, no solution is perfect unless it's possible to exert greater control over faction diplomacy than has so far been seen. You could have various nonsensical situations, such as the Scottish Nobles fighting against both the English and the Scottish Rebels, or the Scottish Rebels fighting the English and the Scots Nobles while the latter was also fighting the English.