Take Alfred developer Andrew Pepperrell, who wrote on his blog about how he's hesitant to release a version of Alfred Powerpack to the Mac App Store that complies with the current rules (the ones that do not mandate sandboxing). Were he to do so, come March, any subsequent updates to the app would necessitate stripping out various features that customers would have already paid for.
Pepperrell rightly points out that customers still have a choice; you can buy his app outside the Mac App Store and avoid the sandboxing question completely.
Mueller's key concern is simple: Customers will be surprised and confused if their Mac App Store purchases get updates that remove prior functionality to comply with sandboxing rules. "And they are going to be mad at developers, not Apple," he added.
Mueller said that he's hasn't "completely decided" just what he'll do with his apps once the March 1 deadline rolls around, though he added, "I'll probably offer less-restricted versions outside the App Store."
Bare Bones's Siegel faces a similar problem: "Our products will need to change in order to comply with the sandboxing rules," he wrote. He pointed out a slew of features in BBEdit that may not be allowed once the sandboxing restrictions are in place -- multi-file search and replace; text factory applications; multi-application automation using AppleScript or Automator; Open File by Name; disk browsers; live folder views in projects; SCM integration; bulk HTML tools operations (syntax check, site update); and lots of behind-the-scenes stuff such as scanning directories for ctags data. "Customers are expecting all of this to work, even in a sandboxed environment, so there are some real challenges there," Siegel said. An open question is which of those features will be allowed by Apple (but with extra work required on Bare Bones's part) and which will simply not fit within Apple's vision of what an application should be allowed to do.
What's more, for many developers, "not selling through the Mac App Store… isn't really an answer at all," according to Siegel. "Unless you're willing to walk away from a majority of your audience. And no sane businessperson would do such a thing."