Under Matt Idleson, DCnU Supergirl probably was stronger than DCnU Superman.
He said as much in an interview. Reign said as much in her speech.
The Supergirl creative staff had her father augment her through lab experimentation, the comics even showed her able to create her own yellow sunlight, so theoretically able to amp herself at will. She'd be naturally stronger for a short time awakening from perfect suspended animation coming from a heavy gravity planet to a lighter gravity one. Her muscles would be used to bearing heavier loads. She might even have benefitted from having a better diet. Explanations abound for anyone who decides Supergirl should be stronger than her cousin, and very good and sensible ones at that.
However, Eddie Berganza is once again editor. So DC has probably recanted that position. For tradition and fear of sales losses, no doubt. A too-powerful Supergirl is a genuinely frightening idea to the company, let alone Superman fans.