Frankly, as Ubuntu's founder Mark Shuttleworth said, neither plan is great, but "Secure Boot retains flaws in its design that will ultimately mandate that Microsoft's key is on every PC (because of core UEFI driver signing). That, and the inability of Secure Boot to support multiple signatures on critical elements means that options are limited but we continue to seek a better result."
There is still another way though: Use open hardware with open source software. This is the path Cathy Malmrose, CEO of the Linux PC vendor ZaReason would like to see followed.
As Malmrose said "With UEFI's Secure Boot around the corner, we are hoping to raise awareness that Linux distributors don't need to sign with Microsoft [or use their secure boot]. Computers that are rooted with open bootloader are available. That's what we ship." True, "UEFI's Secure Boot is implemented at OEM (original equipment manufacturer) level, all new PCs purchased (with the intent of loading your favorite distro) will have Secure Boot."
Malmrose isn't happy with disabling it or using Fedora or Ubuntu's methods. "Yes, you can disable it. But 'disabling' something that's 'secure' makes you bad." She also fears that in the long run, "the keystroke(s) needed to get Linux to run on machines post-2012 will be simple at first, becoming increasingly complex at a non-shocking rate. It's a monumental shift at OEM level." Malmrose fears that this will make desktop Linux "too difficult to new users, [and this will cause] slow death by suffocation" for Linux.
So, here's where we are today with Linux on Windows 8 PCs:
1. Hope that the OEMs will simply let you disable Secure Boot during the pre-boot up. If they do, then installing Linux on a Windows 8 PC won't be much harder than it is today on Windows 7 systems. This will not, however, be an option on Windows RT ARM-powered systems.
2. Use a Linux, like Fedora, that provides a Secure Boot compatible key using Microsoft's own Windows 8 signing tools
3. Use a Linux, like Ubuntu, that provides its own Secure Boot compatible key.
4. Avoid Windows 8 systems entirely and use open hardware instead.
Some Linux distributors, such as openSUSE, haven't decided what they're going to do yet.
I wish I could tell you that it's all going to be easy or give you a magic series of steps that you'll be able to take to get your Linux of choice running on your laptop or desktop. I can't. There will be no easy way to run Linux on Windows 8 PCs and we still don't know how OEMs will be handling Secure Boot.