It's easy to hit Ragna out of 6D.
But anti-airing or air throwing I'll concede isn't an effective way of countering it, due to the hitbox on it, as well as Ragna's position. However, just about every A and B normals (and even things like Jin's 5C) will counter hit him clean out of it's start up off most gatlings if you react correctly. Just like if you react correctly to BS, you can anti-air or air throw Ragna out of it.
5C into 6D or 6C into 6D is your safest bet going into it, as the gap is smaller, but you can still hit him out of it
But let's face it, how fast do people react usually, especially if you're creative with your strings.
Thus, 6D is effective, and Blood Scythe probably will be too, especially with it's easy cross up potential midscreen (which will avoid pretty much every anti-air in the game from the looks of it)
EDIT: You can space 6D really well to avoid being hit out of it, but then j.D whiffs and you're pretty vulnerable to being hit after since they'll recover from blockstun faster than if you made them block both moves. Everything has it's use.