You could have your attorney suggest that this was simply family argument, no one got hurt, and maybe withdrawing the charges upon completion of 120 hours of community service and anger management courses. Or, if you don't want to do all that, you could ask the it be reduced to a summary disorderly conduct if its currently a misdemeanor.
You could file for full custody... for obvious reasons. Then look into getting his parental rights terminated.
I can't really say what will happen with the rape charge but your description of your girlfriend and the rapist should be obvious to a jury. As for you interfering, that would be a criminal charge of intimidation of a victim or witness, which could get both you and your girlfriend in trouble.
Would you qualify for a public defender? Your lawyer is obviously doing thing on your behalf, but not meeting before the hearing is a little unprofessional. You could just see what a PD would say.
If the age of statutory rape in your state includes the age of 16, then yes you can; some states cut the age off at 15 and thereby 16 & 17 year olds can consent to a sexual relationship.