It does not seem like the cyst itself, being only 2cm, would cause that much pain. However, I have read where other women had small cysts and had a lot of pain thought to be caused by the cyst(s). And if the cyst is leaking or you had another one that ruptured, that can cause infection which can cause pain. So I would not be too concerned with the PID comment at this point.
As far as the prior abnormal cervical cells for which a LEEP was done, if the margins were clear and paps have been normal then cervical cancer that could have spread should not be a concern. Ovarian cysts are very common and very rarely cancerous in women who do not have a genetic predisposition for ovarian cancer (lifetime risk being less than 2%).