I'd say that she trusted him with her secret but his subsequent distance from her would have eroded the feeling of friendship she once had for him.
Think about it; she trusts him with her secret but, after he knows that she's got magic, he avoids her. The next time they have any real interaction, he poisons her. Remember that Morgana didn't know that she was the vessel for the sleeping spell. She may never have known of it, as I can't see Morgause feeling obligated to fill her in. She wasn't in the loop about what Morgause had planned, only that she wanted to bring down Uther. From her perspective, there was no reason to believe that her immunity to the sleeping spell was due to anything other than the fact that she had magic. As far as she knew, she was the only one with magic and even Merlin needed Kilgharrah to tell him that the spell needed a living vessel to sustain it. To her eyes, it must have looked as though Merlin, seeing a magical threat, assumed that she must be involved rather than giving her the benefit of the doubt, and that he chose to murder her rather than talk to her about it.
I'd say that Merlin had the opportunity to become a close friend to her had he confided in her about his magic when she first confided in him about hers but he didn't take the opportunity.
Katie McGrath did a great job with the moment in Season Five when Mordred tells Morgana that Merlin is Emrys. You can see the emotions she's feeling at the time and I think that hurt was definitely in the mix. I wonder if she was remembering when she trusted him with her secret and, instead of trusting her with his secret in return, he chose to kill her.