I think it is that his wife was pregnant.
I don't think it was the infection angle due to the time line as someone else noted.
It could also be he told them of a secret installation somewhere else but I kind of doubt that or the the sheriff would have shared it with someone after the explosion...I guess there is still time for that to happen in the next season.
One thing that did leave me hanging with the ending was the Merle (sp?) character. Somehow I thought they would run into him at some point before this season ended. Whether it finding him alive and after them or walking around as a zombie. They made it look like he was still alive and they kind of said that they thought he stole the one van they had but there was no way of being sure of that.
I kept expecting them to run out of the facility before it exploded and while shooting zombies they would shoot merle and watch his brother go crazy and run back into the building or something.