How do you see this working out in the longer term - is there a Secure Boot alternative that allows freedom to boot Linux, yet protects against vulnerabilities like these ?
Any user can simply create their own key, sign their own firmware, linux, and what have you with it, and then boot away.
Unfortunately, Microsoft mandates secure boot but doesn't require the feature of adding keys to be present... so the reality is a bit more grim.
The reality is that most distros have managed to get a signing key from microsoft (and those that haven't, there's a grub shim signed by such a key) that is included by default in microsoft certified secureboots. This has been working, but is not as ideal.
Not really. The barrier to obtaining a signed bootloader isn't that large, and if you're unwilling or unable to do that you can use http://mjg59.dreamwidth.org/20303.html and just oblige your users to jump through an additional (easily documented) hoop. We had legitimate concerns over the impact of Secure Boot on free operating systems, and for the most part we were able to reach some reasonable solutions.
Funny. And here I thought I was secure booting Ubuntu already.
I think this issue was resolved 2 or 3 years ago.