I will be perfectly blunt about this, and I think it is about a 50-50 chance either way. With everything that Allen is going through and everything that he has gone through, I could see it being the death of him. Of course, you can easily say that he has been through so much that he deserves a happy ending.
Due to his personality and his virtues, I could easily see Allen sacrificing his life to kill the Millenium Earl and putting an end to his plans. I can also see Allen helping everyone achieve victory and living through it. Then he would be able to live a normal life that he has helped many other people continue to live (that would include having a relationship with Lenalee).
I even think it is possible for Allen to go through something similar to what Harry Potter and Cloud went through as well and go into a death like state and recover.