Why is it GOG.com has the sequel (Freedom Force vs. The Third Reich) but not the original?

Complete guess: the titles are owned by two different companies.

That is the most likely explanation as Freedom Force 1 was made by Irrational Games and published by EA and Crave while Freedom Force vs the 3rd Reich was self-published and yes I know Steam and GamersGate have the first game but most likely Irrational had a deal with EA and Crave(does Crave even still exist?) where they could sell the game at certain stores, who knows for sure.

...is on GamersGate. Get the sequel here, and get the first game there. It's really that simple. I wouldn't bother waiting for Freedom Force to show up here, if I were you.

Steam lists the publisher as 2K Games, so that rules out FF appearing on GOG for the time being

That's right 2K owns Irrational now..