You are correct that 326 dpi would also have been an option, but while we've seen lots of, say, 1280x800 panels in the wild at the Mini's price point or lower, I have no idea what the pricing of a 2048x1536 panel would look like. As you note it would probably be substantially more expensive.
This just highlights why dpi independence is important - if your only option to raise dpi is to double it, that's not particularly helpful unless you only plan on improving the dpi every other year when costs have fallen sufficiently.
From my reading I think that price of the screen for a 2048x1536 screen, while higher, isn't the real showstopper.
The truly big issue for a very high-resolution screen is power draw requiring a larger battery leading to a larger, heavier device.
As Amazon doesn't highlight—for obvious reasons—the iPad mini is thinner and lighter with a larger screen. This is where Apple's engineering dollars were spent.
Sourcing enough parts could also have been an issue. Perhaps they couldn't get enough high resolution 7" screens fast enough. Having the mini being on back order throughout December would easily cost them many more sales than they lose from people who decide to skip the mini due its screen resolution.
This just highlights why dpi independence is important - if your only option to raise dpi is to double it, that's not particularly helpful unless you only plan on improving the dpi every other year when costs have fallen sufficiently.