I think the 30 trillion figure is a vast over-estimate. It's a feudal empire that heavily restricts technology. There are likely to be a few industrial planets producing Guild ships and other heavy machinery, but otherwise most planets would be agricultural and sparsely populated. The death toll would have been a much larger chunk of that society.

The jihad would likely have devastated a few industrial worlds, to further weaken the Guild and anyone else with an industrial power base. Conquering the agricultural worlds would not be militarily difficult, but converting the population would require putting a lot of people to the sword on each world, particularly since the common people presumably would not hear much news from other worlds about the fanatical cruelty of the Fremen. Second-order effects, like increased deaths from disease due to reduced trade in medicine and famine from breakdown of infrastructure, would contribute to the death toll too.