“I’m curious, what hurts more? Thinking you should hate him, or knowing you don’t?”
Merlin and Morgana are both born with inherent magic, which Uther has arbitrated is Wrong because he is ignorant and vengeful. Uther’s word is law, so magic is illegal. Merlin and Morgana both could be shunned, banished, or killed if they disclosed their secret or if it were found out. This leaves them feeling isolated and unsafe.
Morgana takes the only path she sees available to her: she joins with her sister and fellow magic-user, Morgause. She lashes out at the power structure that is persecuting her and she is willing to fight for her freedom. She is willing to kill Uther because Uther would have no trouble killing her, and has killed countless of her kin in the past.
Merlin, on the other hand, takes what he sees to the morally superior way, deciding to wait and ingratiate himself within the existing hierarchy. If he shows Arthur that magic users aren’t evil, maybe Arthur will change his mind and help Merlin out. This way is much better, Morgana, says Merlin, because no one has to be hurt.
Do I even need to say it at this point? METAPHOR FOR QUEERNESS. I’m not saying it was intended that way, but it’s crystal fucking clear.
Uther represents tradition and the oppressor, Arthur the open-minded successor who might be convinced to bury the hatchet. Morgana is the angry rad-queer who can see the system built to fuck her over but knows she can’t change it by herself, or maybe at all—not that this’ll stop her from fighting. And Merlin’s the cis gay white boy who says everything will Get Better if we show them that We’re All the Same Inside, who says that his way is the only way.
No one can say for sure which way is better, but the latter is most definitely nicer to the oppressors than the former. And just as in the queer rights movement, Morgana takes the brunt of the flak.