99.99% of users will never need to touch those system directories, (They aren't even required for homebrew), and, at the same time, writing to them poses a huge gaping security hole for all OS X users. Locking them down (particularly in a way that can be trivially reversed with a user who has physical possession of the device and the password) is the right thing to do.
For the 0.01% who need to screw around with the operating system directories, they can take the 90 seconds to hop into recovery mode.
This is a situation where 100% of the user community has a reasonable solution, 99.99% aren't inconvenienced in the slightest, and the security situation goes up significantly. It's like hiding ~/Library by default - 99% of users probably don't need to mess around there, and hiding it probably reduced a lot of failure modes. (and, once again, for the 1%, chflags solves the problem in 5 seconds)
Honestly - I've always been terrified whenever I've been asked for my password during installation (I do a gut check every time an ARQ upgrades asks me for my password - "Do I trust them one more time? Well, they are my backup software, so, ...) - What if it's dropping something in my system directory?
I usually follow up with a cd /; sudo find -cmin -5 to see if things look reasonable - but I'm guess not all users do that. Also - with all the extended attr stuff on OS X, it's not even clear that a find -cmin -5 would be sufficient.
So - count me in the group that is really, really pleased that Apple is locking down those system directories by default.