The movie of course ends with Graham coming back to faith. He realizes that the death of his wife served the purpose of saving his family during the alien invasion. His son gets poisoned by the alien being. Then Graham prays to God to bring his son to not die. His son lives.
So superficially the movie seems to be a vindication of faith. The faith represented in the movie partially aligns with the kind of faith that the bible talks about.
Romans 8:28 says that God works all things for the good of those who love God. So in that sense the movie seems to align with Christian faith. In that sense, the death of Graham's wife is something that is worked out for the good.
At the same time, Christian is not outcome oriented. When we pray we are promised answers. But it is also true that God is not some prayer answering machine. God gives us His presence as a gift through Christ by the power of the Holy Spirit. The essence of faith is to believe in God as the loving presence, Jesus as the face of God, and Holy Spirit as the power of God. Prayer is a way of being in God's presence. In Psalm 27 David says he wants to be in God's temple all the days of his life, gazing on Him all the time.
Graham, having lost his wife, is in a state of detached shock. In this he has distanced himself people around him, even his kids. He has distanced himself from God too. The way out of his grief come by his finally getting to a place of address himself to God, the first words he says is, "I hate you." In so doing, Graham acknowledges God's presence. In a sense this way of Graham talking to God is a form of a lament prayer - the Psalms often take the form of lament. These lament prayers is one where God allows the petitioner to just pour our his/her heart to God.
In some ways Graham is going through an experience that is analogous to Jesus saying, "why God have you forsaken me?" which is a quote from Psalm 22, a lament Psalm. The point of the movie Signs is that, at times, our faith we may go through a dark night of the soul. The key in those moments it to keep the communication with God open, channeling our feelings to God, even if that feeling is despair or anger. God works it all for the good. His presence is the best goodness we could ever have!