If you want to come up with an explanation for why Obi-Wan kept the Skywalker name for Luke, it isn't that hard to rationalize. Luke was always meant to be a weapon against the Sith. From the moment Obi-Wan takes him, his destiny is to confront the Emperor (especially since it's unclear if Obi-Wan knows that Vader survived Mustafar at that early point). The Skywalker name is itself a potential weapon in that fight. As much as it calls attention to Luke, and potentially imperils him, it's also the one thing in the universe that could potentially strike fear (or greed, as it turns out) into the Emperor's heart. Even Obi-wan admits as such, when he point out to Luke in RotJ that the Emperor was fully aware that potential Skywalker offspring could be a threat to him.
This would ultimately apply even more so to a confrontation with Vader, I would think.
Hell, the psychology of it almost certainly saves Luke on Bespin. Vader's "I am your father" could just have easily been a killing blow with his lightsaber. And consider, after wiping out nearly ever last Jedi in the galaxy, suddenly with Luke the Emperor wants him taken alive? The Skywalker name made Luke a prime candidate to replace the failed Darth Vader at the Emperor's side. So it probably saves Luke in the general sense as well, in avoiding a kill on sight order.