Taekwondo instructors generally don't have the kind of knowledge you're talking about with regards to identifying muscle imbalance and improving it. For that, you need a personal trainer, someone who's knowledgeable in muscle building and proper exercise form.
Taekwondo itself can develop some muscle imbalance, but in general this should be a pretty minor issue. You're not loading your muscles with weights in TKD, so there's less risk of imbalance. But in TKD, you do practice some moves with greater power and frequency than other moves, and that can lead to muscle imbalances.
Whether the types of imbalances caused by TKD training lead to injury or not is questionable. I personally didn't see myself and others having injuries due to muscle imbalance in TKD. About the only things I saw there that might be due to it would be groin pulls and hamstring pulls. But these were often the result of poor form and lack of proper warm-up. They almost certainly wouldn't occur in "real life" either.
With regards to upper vs. lower body in TKD, this is obvious. TKD doesn't utilize the upper body as much. But this isn't generally what's termed a "muscle imbalance" issue. It's a lot less of a risk.
In general, as an ex-TKD black belt, I still find TKD to be one of the best forms of exercise I've ever done in my life. It has a lot of good things going for it. You can easily just do TKD alone (no other types of exercise) and be physically fit. It improves functional strength in virtually all muscle groups.
The only thing that is bad about TKD, in my opinion, is that it can be very stressful on joints, and this can cause real problems later on in life for some people (some people are more susceptible to it than others). That's okay, it just means you have to listen to what your body is telling you and adjust. If you find your joints are painful after some type of exercise, stop doing that exercise.
Your muscle imbalances will go away if you stop doing weight lifting altogether, since you said you were lifting improperly which caused your imbalance issues. Eventually everything will weaken again. But there's no reason why you have to give up weightlifting. You just have to be smart about it. Find a good personal trainer to give you a good, full body weightlifting program and to look over your form.
If you stick with these four whole-body exercises and stay away from isolation exercises and the "machines", you should eventually re-balance yourself: Dead-lift, bench press, squat, and press. But stick to the proper form!
I'd also add other, complementary exercises to those to balance it out and make it more interesting. Such as: pull-ups, chin-ups, crunches, dips, lunges, step-ups, rows, and Bulgarian split-squats... Look into Jim Wendler's "5/3/1" program. I do that exclusively now and wished I knew about it a long time ago.