Hello! I love discussing stuff like this so comments are welcome:)
I think you are right, Arthur wasn't acting rationally so who knows how much of Merlin's words actually sunk in, nevermind the events leading up to him almost killing Uther.
Merlin might have seen Morgause like he tends to deal with other magic-users; interested but ultimately loyal to Arthur. He's killed other users of magic before for that loyalty, to his own disadvantage (Saving Uther, etc). Hopefully Arthur will realize this (eventually) even when he realizes Merlin has been lying. After all, "Actions speak louder than words" and Merlin's actions with regard to Arthur are not those of a lying sorcerer but of a loyal friend (well, mostly, but you see my point).
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I think you are right, Arthur wasn't acting rationally so who knows how much of Merlin's words actually sunk in, nevermind the events leading up to him almost killing Uther.
Merlin might have seen Morgause like he tends to deal with other magic-users; interested but ultimately loyal to Arthur. He's killed other users of magic before for that loyalty, to his own disadvantage (Saving Uther, etc). Hopefully Arthur will realize this (eventually) even when he realizes Merlin has been lying. After all, "Actions speak louder than words" and Merlin's actions with regard to Arthur are not those of a lying sorcerer but of a loyal friend (well, mostly, but you see my point).