I'm thinking that maybe JJ is going to get taken POW, hopefully not for the whole season though. I don't think they'll kill him, but I'm definitely thinking something will happen--such as POW.
Personally, I think it would be far out of character for JJ to not want to be a dad. JJ, especially since joining the marines, has developed a pretty big sense of personal responsiblity and doing what's right. I think when it's all said and done, he will want to be with Beth and their baby. Yes, Beth and JJ do disagree from time-to-time, but all couples disagree. It is very obvious watching them though that they care very deeply for one another and are crazy about each other.
Just another thought here... What if JJ gets back and notices romantic tension between Beth and new guy? We get more jealous JJ, which totally rocks when he gets all jealous over the thought of Beth being with someone else...