Having had issues with my weight, been anorexic and still suffering from low-level body dysmorphia, I understand what you mean. You want to eat naturally, intuitively, but it doesn't work. So you control what you eat. But that makes you scared you're falling back into ED again. The control doesn't feel right. It feels obsessive. And it scares you.
My fiance helped me understand it, though. Everyone healthy obsesses a little about their food. And it's OK. Because you're replacing a bad habit with a good one. Yes, it's still a HABIT, an OBSESSION, but it's helping you. For example, I went from fat-avoiding and calorie-counting obsessively to obsessing over balancing my water and fat intake and over keeping "cheats" minimal. I went from obsessively wanting to see more ribs (a sign of how "well" I was doing), to obsessively wanting bigger muscles. No, the mindset isn't healthy. But we've managed to put it in an environment where it can LEAD to health.
I don't think you can ever fix it. Not truly. I don't think you can ever look at a bit of fat on your thigh and not think "yuck" or ever avoid wondering if you've eaten "too much" fat. But you can override it. Obsess, but obsess about POSITIVE things, things that do you GOOD. And yes, you'll have ED thoughts, but you can tell yourself, the second you have them: "No, that's wrong. My thigh is fine and the fats I ate were good for me. It's not me thinking that. It's the voice of habit and the voice of worry and I won't listen to it."
I'm having a bad day with it today because I ate over 2700kcals. The voice is telling me how unhealthy it is, how fat I'll get... And I have to keep reminding myself that I did a lot of exercise and a lot of mental work, which makes for a need for more kcals. I keep reminding myself that I'm eating what my body wants, that this isn't everyday, it isn't a binge. I keep reminding myself that one or two days a week don't matter individually. It's hard, but it's POSSIBLE.
You'll soon find the thoughts happening less frequently, or good thoughts happening more frequently.
It's a long road and you probably won't come out of it thinking about food like other people do. But you'll come out of it loving food, loving yourself and only having the occassional doubt.
If you ever have concerns or fears, or just want to talk in general, feel free to PM me. I know where you've been because I'm not really out of it myself. And, whilst I'm no expert, I know it can help to have someone to talk to about these things.
Be strong and brave.
I rarely talk to people about Paleo/Primal, but, when I do, it's when they're NOT complaining about their weight or health.
You see, I don't really "do" pity. And one thing I've learned about people is that they're more open to suggestion when they're happy and stable. When they complain they only ever want pity, not to be advised.