For the average linux user, key signing isn't really a big deal, imho. Running as a user and protecting root without running unnecessary services is your first step, after that it's all kind of iffy.
Signing something from an untrusted source (Having dealt with having to revoke a bunch of Microsoft signed stuff not too long ago, I assure you Microsoft is not infallible) doesn't buy you a whole lot. If you build a driver yourself and sign it, ok. Actually that's probably the best way, download the nvidia driver, sign it with your own one-time key, and voila, even if someone pulls a Folgers Commercial on your driver, they really can't sign it, they don't even know where the one-time key came from.
For a normal user, the effort to try and hack your own signing mechanism seems like it would be non-trivial. Figuring out how to hack a giant 'trusted' signer is a pot of gold at the end of the rainbow. I would not be suprised if there are more compromised signing authorities right now. Flame was signed with a msft key that was actually not meant to sign code, but for several years, since this key was from msft, people happily loaded and ran flame.
I don't really think it's FUD to say trusting your security to the entity that attracts the most attention is not a great plan.
Your points are good, except I disagree that Linux's only beef is parsing PE files, I think that's really the least of his concerns. Msft could deliver up its keys in any form, it won't solve the insecurity of not knowing if your signer has been breached.
Good security is hard, I think that's the main problem with all of Linus's ideas.