Is this a further way to lock down the OS against viruses? Could it also be used to lock down the OS to prevent you from installing unauthorized apps? Could OS X be going down the same path as iOS, where you have to jailbreak your Mac to install anything not from the Mac App Store?
Unless the SSD is write locked, which is highly unlikely, it will have absolutely no impact on malware protection. The intent here is to simply provide a nice performance boost by putting frequently used system files on a drive that is faster than a traditional spinner, without taking the (perceived) write degradation hit of SSDs (limited lifetime write capability).
Glad to see Apple coming out with this option; while not a new, brilliant idea (it's actually been around for quite a while in larger production systems), it is probably a first for large-scale production-run systems, such as Apple's laptop marques.
Great integration work, Apple.