I tend to think of selling to an app store as basically selling through Wal-Mart or Best Buy vs selling direct. Yes, selling direct is higher margin, but it's also got a different set of challenges. For example, you have to acquire customers on your own.

Probably the best way to look at it would be to treat the Mac App Store as a secondary channel. If it was a secondary sales channel, then it's additional revenue and new customers which is a nice to have.

You are probably best off creating your own customer list and selling directly to customers over time away from the Mac App store. Or, you avoid it alltogether and figure out how to sell direct. The only downside there is you have to do your own advertising and use something like Gumroad or FastSpring or some homegrown Stripe solution for delivery and such.

Nothing is perfect and there are tradeoffs to both approaches.