I understand your worry. Lets break it down step by step.
So i see your concern about the cavity formed inside the bone because of removing the cyst. You can be reassured that any space left inside the bone is immediately filled with a blood clot which will then be formed into bone by bone forming cells called osteoblasts. Our human body is a self healing system and no space is just left there.
Next issue i see is misalignment of teeth. See the healing process is slow, so your teeth may return to their former positions in a few weeks and if they do not, you will have to consult an Oral surgeon.
The pain in the morning is more because the jaw is immobile when we sleep. So, there is an increased stiffness in the healing wound which eases as you go into the day.
Rest assured, wait for a few days. Your problems will go away on their own.
Even after 2 to 3 weeks if issues persist, visit an Oral Surgeon.
Next Steps
Consult with your treating Oral Surgeon
Health Tips
Be patient. The body heals itself.