Please let us know if you're still together two weeks after the race. I think running with her is a bad idea, especially if you already recognize that your encouragement came off as annoying.
When my wife ran her marathon (SD RNR), most of my help was delivered pre-race, from travel arrangements to race tips. On race day, I walked her to the start, kissed her, took a photo, then let her go. I drove to the finish and then ran the second-half of the course backward, so I saw her at 11, then at 17 or so. Each time I jogged about 2-3 minutes with her, enough to chat with her, inquire about things like fluids, and give her information about what was upcoming (such as the nice overpass at about mile 21). Then I ran back to the finish and waited for her with my camera. I think this allowed me to be helpful but never overbearing, giving her the satisfaction of feeling like she did it on her own. She considers it one of the best things she has done.
It helps that she's a gregarious sort, and carried on conversations throughout the race with anyone nearby.