Orion would explode hundreds of nukes not only in the atmosphere, but also in the magnetosphere. Several early nuclear tests were conducted there as well, but before we'd invested huge sums of money on a very large number of earth-orbiting satellites on which we've become very dependent.
The propulsion charges would be a lot smaller than the high altitude detonations that caused EMP damage, and designed specifically to produce a highly directional, relatively high-mass and low-energy jet of plasma aimed at the pusher plate. The EMP effect is also highly sensitive to altitude, and firing rate could be decreased or even halted entirely while traveling through the most problematic regions.
It's not something that we'd want to use regularly, but with the sheer amount of payload available, a single launch could put up enough equipment to establish extensive orbital infrastructure, greatly reducing the mass that would need to be launched subsequently (whether on Orions or on conventional launchers). Being able to produce propellant, structural components, and photovoltaics from orbital or lunar resources would make solar power satellites actually practical, which could then replace fossil fuel power. Refueling and reusable orbital tugs would greatly reduce the size of the rockets required to deliver a given payload...just refueling roughly halves the required size. In addition, many launches would be reduced to specialized low-mass components that can't be fabricated in orbit, and orbital transport and deployment infrastructure would greatly simplify the satellites themselves.
So it's not so obvious. It's not justifiable for a single-use payload (apart from some exceptional circumstance such as preventing a large asteroid impact, predictable long in advance) or for regular use, but the first Orion payload could provide a substantial environmental and economic benefit to offset the launch. A second launch would provide far less benefit, however, and the third even less...establishing infrastructure that immediately renders the launch system obsolete is about the only use I can see for ground-launched Orions.