Hmm, I've only just noticed this but see no mention of it being a problem anywhere. Guilds work independently from factions?!
That seems to totally undermine the idea of factions, especially when 2 are supposed to be at war. What happens when it comes to guild owned assetts, like stations and cap ships? I can understand a player being able to switch allienges, but to have guilds totally ignore them wouldn't work well imho. My suggestion would be to make them faction confined.

And possibly also the chance to go independent of all factions? Thus be able to join an independent guild of say... pirates?

Arrrrr....