It's not attempting to be deceitful. The problem is the DOD has 8x as many employees as the next largest agency. If spaced without a logarithmic scale, the rest of the agencies are so insignificant it doesn't have any effect at all.
To try to avoid the confusion, I'm working on another graph of percentages working for each agency, and a disclaimer about the scaling.
I personally think the author did this because otherwise the DoD would so heavily dwarf everything else that you wouldn't be able to see whats going on. But I agree, intended or not, this has the effect of heavily exaggerating the proportion of people on furlough. Its like using a log scale on a pie chart. It really makes no sense.
The author really should consider this and think hard about what point he is trying to make with that chart on the bottom.
To try to avoid the confusion, I'm working on another graph of percentages working for each agency, and a disclaimer about the scaling.