Two likely possibilities haven't been mentioned yet:
It's probably proportional
Kryptonian strength is usually described in relation to human equivalents (that is, Superman isn't terribly "super" among his own people). Even if Kara's physiology metabolizes sunlight more efficiently than Clark's, she's still substantially smaller and less muscular than he is, so she might still end up being weaker.
If I'm getting a 200% boost to a natural strength of 10, and you're getting a 300% boost to a natural strength of 3, I'm still ultimately going to be stronger than you.
Toughness isn't purely biological
I know plenty of 90-pound girls who can take a punch to the gut without flinching, and I know plenty of body-builders who cry when they get poked with a syringe.
Kara is Kryptonian, so she's "tough" in the sense that it takes a lot of force to damage her biological tissues, but mentally and behaviorally she's still a normal, teenaged girl. By contrast, Clark grew up working on a farm, and has spent years (decades?) fighting and pummeling incredibly tough opponents in one-on-one combat.
It could be that Kara is stronger and tougher than Superman statistically, but her inexperience and lack of combat training prevent her from being as effective in a fight.