I doubt that’s going to happen.
E-readers are extremely cheap even now, and they’re just gonna get cheaper as more people jump on the bandwagon. Add in being able to read on any phone/tablet/etc, and you’ve got even wider of an audience.
The used book market will probably be hit, but the flip side of that is that the new book market is changing as well. Amazon always has at least 100 books for sale under $4, as well as “Kindle Daily Deals” that are quite good. I buy at least a couple books on a whim for $2-$3/each per month. I’ve found some REALLY great reads that way.
It’s also a lot easier to self-publish these days, and smaller presses can compete better with the Big Guys. Now, I’m not a huge fan of self-publishing - there’s a lot of crap that should never see the day out there - but there are some great examples of self-published books as well, things publishers passed on.
As far as publishers messing with content and ownership rights, not sure what you mean by that. You’re not talking about the one time Amazon (not a publisher) removed and refunded a book that was being sold by someone who did not have rights to sell it, are you? It happened once, it was clearly someone selling something they had no right to sell, and everyone got their money back. And Amazon got so much flack that they’re probably never going to do such a thing ever again.
Anyway, as far as the OP’s question, my opinion is not so much that e-Books killed the big bookstores, but that books turned out to be an extremely good fit for Internet marketing. A lot of people - including me - find it a much superior way to purchase books. I can read multiple reviews before buying from Amazon, I can download and read the first chapter if I want, and I don’t really have to worry about whether or not Amazon has a copy in stock - their inventory is larger than any brick-and-mortar store ever could have. The only real drawback is time & cost for shipping, and if you have an e-reader, that goes away.
Personally, I don’t miss “real” bookstores at all. Online purchasing is better, hands-down, at least for me, and I suspect their success is due to me not being in the minority in that opinion.