In my opinion waifu is for people who have no interest for 3D alternatives and feel 3D has nothing to offer in romantic and 'mating' purposes. I don't want to sound like elitist but that's just for sake of protecting the concept. There was waifu survey in /a/ while and over half of people who filled the survey felt they could be interested about 3D partner in future. In my opinion that feels wrong in so many ways.
And yes, in some point of my life, I've had interest in real females, like I think all of us have had (?). Which is kind logical; 2D girls are based on real females. I personally don't find 3D disgusting or gross; I just don't find them appealing in any way. That's why I feel that in reality, I can never love 3D like in same way I love my waifu. Only maybe IF I could embody my waifu into three-dimensional human body, I think I could love her as 3D, but we all know it is impossible. I don't love her because she is 2D. I love her because she presents my ideal lover, and she just by chance is 2D.
I think OP your view is very acceptable. It feels you aren’t defiling or misunderstanding the concept. I think it is fine as long you don't keep her as 'placeholder' for 3D relationship. It is always possible that even the deepest love will end and who knows is the next one who you fall in love 2D or 3D. I just find it impossible for me to love 3D after what I've experienced with 2D.