DC's canon differs between the comic books, the cartoons, and the movies. Just look at the various takes on Batman.
Concerning the episode in question there is a brief synopsis here at the Dc Animated Wiki which notes that this is not the same Solomon Grundy that they have met before but a creature filled with nothing but rage and chaos magic. As Amazo blasts Grundy, he suddenly realizes there is a problem. From the episode:
Amazo: Something's wrong! The creature is somehow feeding on my energies. He adds my power to his own! My presence here puts you all at risk. I will retreat several light years distance until I can determine how to counter this effect.
This wasn't so much of a de-powering of Amazo as it was a way to get Amazo out of the picture. This allowed Shayera Hol to make the ultimate choice to end the problem of Grundy.