I've thought along the same lines as some of you, but just a little different. I've always seen this line as being about the narrator underestimating the power of God, or love-however you want to think of it. He thinks God is vulnerable, small, and limited in what he can/has/will do, so he goes about doing things himself thinking he needs to help God out.
The lines that come before this one talk about the narrator being able to stand up for hope, faith, and love. The next lines imply that the narrator has confidence (certainty) in his own ability to stand up for these things because as he said earlier, the DNA lotto left him smart, but that in doing it by himself, he is "helping God across the road." He wants to "get over" certainty-his own sureness in his abilities and capabilities-and turn it over to God to see what he can do. It seems that he wants to let go of his attempts to be in control (MOS), and let God do more. He should let God help him across the road like a little old lady, not the other way around.
It also seems connected to the album in general in the sense that sometimes some people who place limits on what love can do become pesimisstic and despair about the future. The whole album seems to be divided between narrators who have had this attitude and narrators who believe in everything love/God can do. This limiting, despairing attitude seems to be shared (though they may be at the moment of change) by the narrators of MOS, UC, WAS, COL, NLOTH, while the narrators of Magnificent, Breathe, SUC, GOYB, IGCIIDGCT, and the girl in NLOTH are trying to tell them to fight against that attitude. FEZ might be someone who is in between these two. In fact it seems on some of the songs that the verses are the person with lack of hope and love, and the chorus is a response to that.