Squats are a closed kinetic chain exercise, training the entire posterior chain (calves, hamstrings, glutes, adductors, spinal erectors), in co-contraction with your quadriceps, abductors, and abs. If you're doing proper, below parallel, knees-out squats, you won't be developing any muscle imbalances in your legs.
The Starting Strength training program and Stronglifts 5x5 both advocate squats being part of every lifting session.
Both of those programs also include deadlifts, not really to address muscle imbalances, but to engage a lot of the same muscles worked by the squat with much heavier loads, and some extra emphasis on the back.
Starting Strength also includes Power Cleans, also not to address imbalances, but to develop power from the legs and hips (instead of just strength).
I mention these programs because they are widely considered to be complete strength training programs, and they focus almost solely on the squat for strength training of the legs. Variants of the Starting Strength program even have deadlifts placed only every 5th workout (see Chapter 8 of the 3rd edition).
If you want additional exercises to assist you in your squats, Starting Strength suggests glute/ham raises, but only in as much as it will assist the main lift, and these are not suggested until your squat has developed quite a bit on its own.
Noticing that you're starting using medicine ball squats rather than a barbell, the only difficulty will be progressively loading the exercise to make it more difficult each workout. You can try heavier medicine balls, switch to dumbbells or kettlebells for a goblet squat, do them more explosively (jump squats, for example), and dumbbell single-leg squats.