First of all, Smallville is not a part of the DC Superman canon and this episode is a hot mess.
Here are some of the problems:
The episode in question is called Pandora and in it Zod has Tess build him a “solar tower” which in reality takes yellow sun radiation and converts it into red Kryptonian radiation which gets transmitted to satellites and beamed back down to Earth.
This apparently gives Zod and his Kandorians super powers while leaving Clark powerless under the red radiation. (Huh?)
When the solar tower was destroyed, this gave Clark his powers back and de-powered Zod. However, Alia still had super speed.
Blue Kryptonite only takes powers away, which is why earlier, Jor-El zaps the orb with blue K.
So, what's going on?
Tess mentioned that she helped Zod into power. So, perhaps Tess used some LexCorp technology during the conversion of yellow to red radiation to overcome blue K and red radiation to give the Kandorians powers while taking Clark's away.