You're right, it does come off as arrogant to say that it's that much more efficient, and that that justifies making this decision. I think that the potential for doing good plays into any moral decision, though, so I don't think it's out of place in trying to explain my rationale. My intention definitely isn't to pat myself on the back here.
It is more efficient and that does justify the decision. Consequentialist ethics runs on quantitative considerations rather than right-of-way, so "it's more efficient" isn't an absolute right-of-way that would mean that you ought to do anything efficient regardless of the consequences - a lot of deontologists have trouble comprehending this - and if Craigslist were acting differently, or Padmapper, "efficiency" might not be enough to make it right. If Craigslist had their own version of the service, or they were about to roll one out, then efficiency wouldn't make it right. In this case, though, I'm willing to say that Craigslist doesn't have a moral right to prevent there from being a better UI to the renter's market, which is a key system resource even if they happened to create it. How would you feel if there were a private company that had invented DNS, taken on the task of gathering DNS data from many submissions, done it ad-free for a few years, and then they started deleting sites they didn't like from the Internet and suing anyone who tried to scrape their data and add the missing sites back in?
Okay, and how would you feel if there were a company that claimed the DNS system was an insecure mess (or maybe one with centralized power at ICANN, a single US organization, and thereby had US-centric agendas), developed a replacement for DNS, initially passed through to the underlying DNS network most queries but added additional features on top, eventually got to the position where most DNS queries were going through them (with lockin to the specific extra features they added), and then played the same game you are bothered with (which, I feel the need to point out, isn't even what is going on here: CL is not "deleting posts they don't like" with PadMapper "adding the missing sites back in"... attempting to draw a parallel to censorship in your argument is downright disingenuous rhetoric)?
There is no reason to believe that PadMapper would not easily end up in the same position going forward, and in fact the incentives are sufficiently poor that it seems like a bad assumption to believe that it would not happen: it, at least, has to be considered. To the extent to which you might argue "the conclusion wouldn't happen with PadMapper", it seems even easier to argue that "the conclusion didn't even happen currently with Craigslist" (again, read my earlier parenthetical).
I bring this up to point out that there is an underlying assumption in your argument that presumes the result: that you already don't like Craigslist, and that that is what causes you to like other people over Craigslist. The DNS argument can be used in either direction: the only pull it has is an appeal to things the listener already might like or dislike (in this case, liking the idea of a theoretical open DNS system, and disliking the idea of hypothetical censorship).
