Contrast this with Gryphon, who:
(a) knew Kara was coming,
(b) has about 400 years of experience on Superman,
(c) has multiple children, both biological and adopted, who
(d) have all gotten into the heroing business, quite successfully. Between him and his circle of friends, he could write "So Your Child Wants to Be a Galactic Hero". Speaking of which:
(e) He has a tremendous support structure. Superman may have had some super-friends, but at the end of the day he had to hide who he was from the world and its governments. Gryphon basically is a government unto himself, and he literally has an army at his fingertips, and several others within easy reach (WDF, CFMF, GENOM, the Autobots, Salusia, etc). Plus, Kara herself made a number of super-powered friends on her first day, friends who would, and did, fight for her. Add to this the fact that:
(f) He is not as frightened of his children dying as Superman was. That may sound callous, but it's a statement of the fact that he knows they can handle themselves, he has faith in them and their friends, and even should the unthinkable happen, the doors of death are not closed to him. I'm sure he doesn't consciously rely on this fact, and Kei's disappearance may have shaken his faith in it, but if Kara were to die in battle, he'd weep and grieve, and then take a week-long vacation to visit her in Valhalla.

So yeah, don't hold it against Clark that he was overprotective of Kara. It's like comparing apples and cybernetic ultra-oranges.