It is not good for the female to carry joeys before she herself is fully grown. Nursing joeys can pull a lot of the calcium she eats for milk production instead of her body using it to build strength in her own growing bones.
There is no reason to separate them since they have already been together and both may be depressed if they are kept separated.
You do need to read up on breeding and how to care for rejected joeys if she does become pregnant. This web page has a wealth of information
http://www.suzsugargliders.com/educationalarticles.htm
Your best bet is to go ahead and have the male neutered and hope that she is not already carrying joeys.