Just another speculation in this long hiatus. In 2.08 Secrets and Magic, Anthony Head said that there was more to the back story between Arthur, Uther, Ygraine, Morgana and Morgause. In Legends, Morgana and Morgause are full sisters whose parents are Gorlois & Ygraine. Arthur is their half-brother - parents Uther & Ygraine. In Merlin, Morgana and Morgause are half-sisters. Do they share the same mother or father? Morgause gave Morgana a bracelet which she said was from her mother. Gaius recognised the bracelet as from the house of Gorlois.
I hope that Morgause is Arthur's half sister. If so, maybe Uther had an affair (in his despair of Ygraine's inability to conceive) with Gorlois's wife, mother of Morgana. The affair resulted in Morgause. In his guilt, he wanted the baby dead. Morgause knows this and that's why she hates him and wants him dead. Plot holes: Uther did not seem worried / guilty about Morgause - only that Morgana would not find out about her connection and Arthur his birth. Uther said he thought the baby was dead, it doesn't mean that he wanted the baby dead. But then why did Gaius have to secretly give the baby away?