Supergirl, arguably, has always been a bit stronger than Superman. (She doesn't hold herself back as much, Superman "pulls his punches" a bit due to his human upbringing. Kara doesn't have that upbringing as programmed into her since she came to Earth as a child.)
Not stronger, but yes, you're right about the pulling punches thing. That was even brought up in a comic where Clark had to at one point put his foot down and pull his punches a little less against her.
This is also a point that could have easily been brought up in the episode, but the writers chose instead a worse direction.
To get back on topic, compare this to the treatment of Wonder Woman, who didn't need to show strength by making another heroic character look weak. They didn't even do that with Steve Trevor who is no Superman.
Steve Trevor was every bit the hero and badass that Wonder Woman was--just without the god like powers. When she saved his life, he didn't look weak. He was in a bad position, and as good people do, Wonder Woman helped. The writers created situations that didn't require Wonder Woman to show her superiority over Trevor, even though she was the star and the main hero of the story.
Having Supergirl fight Superman was just a bad idea. It wasn't necessary to have Kara involved in the big showdown with Rhea, just like having a woman president in the episode before didn't require a man-hating speech by Cat Grant to show that a woman can be a good leader.
If anything, they weakened Linda Carter's character because she was about to go all badass on Rhea.
Supergirl's story was told by writers that had a chip on their shoulder. Wonder Woman's story was told by writers that did not. The difference was tremendous. And I say this with 100 percent faith in the Supergirl writers that they are much better than that.