To begin with, the military's practice of not refunding the $1,200 contribution is legally shaky. However, it is highly unlikely that you will want to fight an appellate battle against the U.S. government for a mere $1,200. So you won't be getting a refund.
There could be a way to get a discharge and get at least "month for month" benefits, meaning that you would get GI bill benefits at the rate of one month for every month served. You did not make it clear, but you did not say if you pressed charges for rape. You may want to consider it. First of all, the person who did it need to be dealt with. Secondly, if you can establish that you were the victim of a rape there is an exponentially higher chance that the military would agree to grant you a "hardship" discharge that would allow you to keep some benefits, as opposed to a voluntary parenthood discharge that will strip you of GI bill benefits. Legally speaking, when you take that voluntary discharge you are giving up those benefits.
There could be a way to get a discharge and get at least "month for month" benefits, meaning that you would get GI bill benefits at the rate of one month for every month served. You did not make it clear, but you did not say if you pressed charges for rape. You may want to consider it. First of all, the person who did it need to be dealt with. Secondly, if you can establish that you were the victim of a rape there is an exponentially higher chance that the military would agree to grant you a "hardship" discharge that would allow you to keep some benefits, as opposed to a voluntary parenthood discharge that will strip you of GI bill benefits. Legally speaking, when you take that voluntary discharge you are giving up those benefits.