So assuming our cleric casts desecrate and attempts to reanimate a Storm Giant (19HD) which starts below the 20HD threshold of not being animate-able but adds the skeletal champion template to that (which adds 2 HD making the total 21HD) prevent the Storm Giant from being reanimated as a Storm Giant Skeletal Champion?
The Skeletal Champion template is a separate and distinct template to the Skeleton template. It is the Skeleton template that has a maximum of 20 Hit Dice, not the Animate Dead spell or the Skeletal Champion template.
Having said that, without some other ability, I don't see any way to create a Skeletal Champion with Animate Dead, with or without Desecrate? Or any other variant Skeletons other than Burning and Bloody Skeletons, for that matter.