First, when Road "threw herself at him" she was yet to "take a bullet for him". So Allen had nothing to feel obliged for and still, he let Road hug him, he even closed his eyes. Do you usually close your eyes and let relief, moreover, happiness spread all over your face when someone you don't like hugs you? Well, I don't.
This is DEFINITELY not an expression of indifference.
Also, during the escape Allen held Road, pulling her into Tim's mouth and such. Road was unconscious, he could have just left her to Tykki or something but even after they landed (ch. 204, page 26) Allen held her in his arms.
Um, yeah, one more thing. You state that Allen has never really pushed Road away but that's not quite true. When Road kissed him, he DID try to push her away. Also, Allen looked absolutely shocked then. And now? He just leans into the hug, closes his eyes~ No shocked expression, no mark of "indifference" on his face. I guess that's how blossoming love is. :>