I was re-watching "Truth, Justice and American Way" from Season 1, which is the one in which SG is put into a cage under the red light. After being in it for a few hours and then the yellow sun only shining on her for about a minute, she was able to storm out of the cage and beat down on the bad guy pretty easily. So, the only thing that should have made her that weak would be the blast from Metallo as Leila stated.
It would probably have been easier to make that connection if it had been written differently or if they were consistent in how kryptonite affects SG.
I understood that the prism they were using was a stronger more focused amount of Red Sun, AND, we really have no timeline as to how long she was under the influence of the red prism in the crossover. ALSO, having been hit by Metallo, full on, then hit again with the rest of the group would have weakened her considerably giving the red prism even more of an impact. As far as the earlier episode from Season 1, we don't know what she was hit with for him to take her out in the first place because of the poor editing of that episode, but we do know that she was under the influence of the red sun far less time probably than she was in the crossover. IMO, the biggest difference was in the Episode from Season 1 it was "only" the red sun, whereas in the crossover it was her being hit twice by a massive amount of Kryptonite, AND the power of the energy being put through the red prism. So, I can see the difference between the 2 episodes, they really are apples and oranges so to speak.
Yes, I believe that we're saying the same thing, from what I can tell. That is was the blast from Metallo that weakened her, not the red sun. The red sun would not have weakened her because we know that Krypton's own sun was red. The lack of effect from the red sun (energy wise) to her was shown in the Season 1 episode that I referred to.
I think it was confusing, at least for me, because of the writing. They kept emphasizing the red sun affecting her (which it did as far as letting them cut into her). That emphasis along with a lot of other stories/actions/characters going on simultaneously, allowed the Metallo blasts to get lost along the way; thereby, losing its effect on the viewer.