Mildly off-topic but I am still not clear why people choose to have the OS partition(s) encrypted. What does this protect? While running, it protects nothing, same as the end user data, but if a disk gets physically stolen it protects against data loss, but it's an OS so that's the part I don't understand. I fully understand protecting end user data with encryption in case of a physical theft.
I was thinking about that for a while, and came to the conclusion to
not encrypt the root - mainly for convenience reasons: I want a basic singleuser OS to come up in case of problems, because that is my main toolkit to fix the other things, eg. rc.d issues, hw issues... and in such a case, when there are problems already, I don't want to bother with other things, like broken CD readers, usb boot support gone fishing, or encryption.
But I found there is quite a lot of things to be taken care of. As
SirDice mentioned, there may be stuff spamming
/etc that do not belong there. But then there is also the issue of
/var. The OS wants /var to be there,
vi doesn't run when it is missing, other things may, too.
So you have to look into there, understand what all that stuff is good for, and devise a solution. Maybe having a limited /var directory on the root filesystem and overmounting during boot (which may bring other problems).