1 - What happens to a Jena follower in a Kami guild (and vice versa)? (Bearing in mind that belief needn't equal fanatacism and many hominists still adhere to a milder form of their faith).
They go "unspecified" along with the guild for some amount of time. Eventually you'll have to choose one way or the other
2 - Can people with different civilisation affiliations join together in a single guild?
Not if they are "citizens"
3 - Who can and can't join a neutral guild?
Only players neutral to the race/cult the guild is neutral too (if the guild is race&cult-neutral, only race&cult-neutral players can join)
4 - Who can and can't join a civ affiliated guild?
Players who are citzens of that race, or race-neutral players
5 - Who can and can't join a religion affiliated guild?
Players who are converts of that cult, or cult-neutral players
It seems to me these rules are based on the character's own set of morals (that the player doesn't get to enforce) - a race citizen will only join a group who hold the same views as him, not a neutral one. Most people on these boards seem to take the "guild" view of things (ie as a guild they will only permit/refuse certain citizens... I can't quite explain this right but its kind of the difference between character-centric and guild-centric)
Because of this "character-centric" way of doing things, your questions are much easier to answer when posed as "what guilds can a race citizen join?" or "what guilds can a race-neutral player join?".... at least to me anyways