Three facts that we know from Sins of the Father:
1. Morgana and Morgause are both considered to be of the House of Gorlois
2. Gaius thinks/knows that they're half sisters.
3. For some reason baby Morgause needed to be smuggled from Camelot for her own safety. Gaius feared what Uther would do if he didn't.
However fresh news has made this more 'interesting'. And whilst, at first, it seems designed to upset some shippers, all may not be as it seems.
From Richard Wilson's DS interview we know there's a secret about Morgana and Uther that even Gaius doesn't know.
Taken together, these pieces of information seem to cause big problems in how these two girls are related.
First possibility is that they have the same father and different mothers. The two candidates are:
This would tie in with them both being of the House of Gorlois and the fact that clearly Gaius believes that Gorlois is Morgana's father. Their different mothers in this scenario could be due to the fact that Gorlois's first wife (Morgause's mother) died and he remarried and they had Morgana. All is fine - Gaius would certainly be aware of this - except we have no obvious reason with that why Morgause needed to be smuggled out. This could be worked in if, in fact, Gorlois's first wife was Igraine and, like in the legends, Uther essentially 'stole' her (although perhaps here she went willingly). That would certainly explain why he wanted baby!Morgause out of the picture. If Igraine found out she was already pregnant after re-marrying Uther, it would be much easier for him if the baby was gone. Gaius could certainly know about this scenario BUT it doesn't explain what secret there could be between Morgana and Uther if it is regards their relationship as heavily hinted. It could possibly, however, be referring to the manner of her father's death and hence why he feels the need to look after her so much and why he seems uncomfortable when Gaius speaks of Gorlois - basic guilt. Lastly, there is a possibility that Morgana is Uther's niece, the daughter of his sister most likely. This can work with all the known fact, but it is obviously harder to have a secret about who the mother of someone is rather than the father.
Uther could be the father of both. It is extremely unlikely that Igraine was the mother of either of them because why on earth would that be hidden? Morgause being his illegitimate daughter would explain why she was smuggled out. And perhaps he gave his second illegitimate daughter (Morgana) to his best mate to bring up as his own. But this does beg the question how the hell does Gaius think they're related? Does he think they're both Gorlois's daughters (and did Uther actually have affairs with two different women who were married to Gorlois?!). Does he for some reason believe they're from the same mother - but who does he think the different father's are? He can know that Morgause is Uther's daughter, but clearly he does not know that Morgana is Uther's daughter if that is the case... This idea can work - just - but it is very complicated!
The other possibility is same mother:
Could be that she had an affair with Uther hence, they have different fathers. BUT Gaius would then think them to be sisters, not half sisters. Unless Gaius thinks she had an affair with someone else entirely. But again, that starts to get complicated and doesn't at all explain why Morgause had to be smuggled away (what problem, pre purge, could Uther have had with Gorlois's daughter?).
Turn it on its head a bit and it could be that Igraine had an affair with Gorlois, Morgause perhaps being a daughter from her first marriage. Could work pretty well actually. Would explain why Uther was keen for Morgause to not be around and also perhaps what the secret is (he found out and killed Gorlois). Gaius would have to at least know about their parentage and realise that Uther knows, but he would necessarily know about Uther's revenge.
Uther's sister perhaps bit of a loose woman (in terms of the era) and had affairs with two different men. Morgause gets rushed away to protect her reputation. The second time, Uther lies about who the mother is and gets his good friend Gorlois to step in (or maybe he's the father and the sister died in childbirth). Again though, this has the problem of how do we reconcile the fact that Gaius knows them to be half sisters yet Uther has kept a secret from him as regards Morgana.
There is also the potential that they are full sisters. For example, both daughters of Uther and some woman (Igraine? Gorlois's wife?) and for some reason Gaius thinks Uther is father of one of them and not the other. But that's a little crazy. Although with these writers...
The last possibility is that they're not related at all. Everyone who is in the know believes that they're half sisters, Gorlois's children by two different wives. But Uther secretly knows that he is Morgana's father. This works perfectly, but again though, what about Morgause made him want rid of her from birth?
tldr version: If the show doesn't intend to retcon entire scenes from series 2 then we know that Gauis believes Morgana and Morgause to be half sisters, presumably both daughters of Gorlois with different mothers, and that something about Morgause's parentage meant she was in danger of Uther having her killed. IF Uther is Morgana's father as heavily hinted, then it starts to become very difficult to reconcile all these fact. There is either going to have to be some very complex relationships and lies going on here, or they're going to have to throw last year's canon out of the window.
It works out much better if we eliminate the idea of Uther being Morgana's father and go with the idea that he killed her father, Gorlois.
Anyone's thoughts or comments would be thoroughly welcome because, as you can see, this is way complicated!