As long as amazon don't ban alternative apps from been able to read drm-free or non-amazon format ebooks, I don't see too much of an issue with it.
It's their device, if they want to focus their attention on supporting their own store/format that's up to them. If users feel the experience offered by epub or other stores is superior to that of the apps that ship with the device, they'll install the app needed to use it/them. If users feel Amazon are going out of their way to make it difficult to do that, then I'm sure customers will start to look for alternatives in the future and it'll start to bite amazon on a HW level (as long as amazon continue to make kindle apps for other devices). I can't say I liked having to use wordpad or ms paint when I used to use windows, so I bought/installed better apps
Really it's no different to Apple pushing ibooks on the iPad. You can still download alternative apps to read kindle books or other formats/stores.
The issue I do take with Apple (don't have a fire, so I'm not sure if this also applies to Amazon) is the requirement for in-app purchases to always go through apple, so you can no longer buy content from within the kindle app unless 30% of the price goes to apple. In a way that problem is made worse by the locked nature of the device and inability to load apps from anything other than the Apple store.
It's a shame devices are locked to a single store though, but as long as apps are not arbitrarily blocked (which they often are) it's not as bad as it could be. I hope we see more open devices in the future, no problem with an Apple or Amazon store shipping by default, but customers should be free to buy apps/content from any store they wish and have the ability to run signed or unsigned code if they want to disable the added protection signing offers. (i.e how current versions of OSX work but on the tablets)