I don't see that as the case. There is malware out there
in torrent land, sure. But if you acquire software from
reputable sources (like a paid app store, referral from
a friend, heard about it on a forum like HN, package
repository), malware just isn't a concern.
Are you kidding me? Have you missed the large number of browser-based vulnerabilities, from Flashback and MacDefender, to the huge number of vulnerabilities the latest Safari fixed?
Would having a sandboxed app store help with any of these? The point I think he's making is that a curated app store isn't going to be a significant malware source.
I don't think that was his whole point. He's speaking in much broader terms in his first paragraph, which is what I quoted. He does make mention of reputation and the app store specifically in the second paragraph.