The DoJ isn't human and is not subject to emotions like "pride" or "embarrassment." Their goal is to win cases and enforce laws, and if the bureaucratic cost of adding more charges improves their chances of having the defendant found guilty on them, they're successful.
The DoJ is part of the executive branch, and ultimately answerable to elected officials who absolutely are sensitive to embarassment. No one wants to see a headline like "FBI wastes $2M on failed prosecution of harmless nerd" when it could be "Hacker gets jail time and fine". So they're throwing mud trying to get something to stick. If it looks like anything does, they'll offer a plea again.
You can't really believe that politics have no impact on the case decisions in the DoJ, can you?
