This article did bring out a couple of important points about the complexity of calculating actions. The sequestration concept is one that gets ignored when people look at only a very short term release. To compare the carbon input of lighting or fossil fuel that has been sequestered for millions of years to the short term ups and down that are measured in days to decades of agricultural activities is misleading.  When the long term sequestered products are added to the normal biological actives is where problems come in.
The ecological impact is also not accounted for.  The ecological impact of cutting rainforest for grazing is large but the replacement of grazers is small and may be positive in terms of ecology.  Many square miles of monoculture beans or oats is harmful to the environment so grass feed beef is better than feel lot beef but it may also be better for the environment than people consuming beans and oats from massive monoculture.