I don't think they made Sylar look weak at all, they just let up a tinge on the speed in which he defeated her. He still completely demolished her physically and emotionally.
Also, while the writers wanted her to be manhandled, they wanted to show that there is at least something in her that can be toned into a fighter. Had she gone out like any other Sylar victim, we'd dismiss Claire as a potential strong character down the road.
Also, I believe Sylar was still recovering and not yet at full power from the end of last year.