Interesting idea, but I see two flaws with that concept on a "full" desktop OS. One is the obvious, if malware takes that scanner out or tricks the scanner into thinking a file is good then it's rendered useless.
That's why the scanner doesn't need to be local but in the cloud, or at least somewhere that nothing can ever touch it.
For me the bigger problem would be performance though.. ChromeOS is basically a browser and is quite lightweight, so there wouldn't be that much to scan. Waiting on a complete system scan for a full blown desktop operating system is going to have a huge hit on startup time, regardless of which OS it is. I'd be willing to bet something that like would get disabled by the majority of users just because of the inconvenience of waiting for a few minutes for their system to boot versus a few seconds.
That's why I say people chose convenience over security. You only boot up once a day, so what if it takes a few minutes?