Although Apple wasn't explicit, I believe only the $30 upgrade from Snow Leopard to Lion is exclusive to the App Store.
The App Store doesn't exist in Leopard and Tiger, so Apple will probably release a full price DVD set for $180 that includes Lion, iWork, and iLife.
Not exactly great, but it is an alternative if you don't want to download from the Mac Store. Keep in mind, prior to Snow Leopard the OS X upgrades were $130 anyway.
I believe they made it fairly clear that the only way to get Lion will be through the App Store, though I don't recall the exact wording during the keynote. What I'm trying to say is: I came away with the impression that the App Store was the only way to get it; could be wrong though.
I suspect it will raise enough hackles.