first and foremost thing, stop getting tensed about having to have to sex. you know what I mean? Do not try to have sex so as to get her pregnant. Untill and unless her periods become normal it is highly unlikely she will get pregnant. so untill that time relax and have sex only whenever both of you feel like and get to know each other better.
From what you describe, she seems to be having some vaginismus
problem. Search the internet for this term and both of you read it in detail. If that doesnt help to solve the problem get in touch with a good lady sexologist
All the best