A lot of people dimiss it as a "crush" or "first love," but they have to see that while it is her "first love" situation, she's mature enough to know her own heart and trust in it. I think when Aoshi "changed" it wounded her a lot more deeply than she showed. After all, he became withdrawn to the highest extreme, and this cut off most of her contact with him. It almost seems like she needs him around, whether it be for strength, moral support, or just being near him. Without someone to protect and love, Misao would be like a stray cat.
And you know what? The relationship is pretty one-sided until Kenshin rips him a good one (uh, literally). It would have been impossible for love to grow in his heart while his environment and feelings were so hostile. And, in the end, even Kaoru notes that his change in demenor has resulted in him finding some inner peace. Kenshin and Kaoru both know that only Misao will be able to fully heal him with her love and undying loyalty to him. After living through such tragedy, she's his last hope.