This problem has been the bane of my existance for at least a year with Sabayon. I just do a layman -s sabayon and rely on emerge after a fresh install. I just gave up.
Seriously don't bash the new users for giving up on this in desperation. I've seen it too. It's a replicatable defect.
I am an experiened linux user who has many many years experience with Gentoo. I'm assuring lxnay (yes I loved his RR4 disk) that there is a defect here. I don't know how the maintainers are using entropy but I just installed Sabayon 4.1 - and did a equo update; equo install equo; equo world and it was all over just like the above when merging python. Of course i fixed it by using the package files using bzip and tar... but that's not the point.
Why can't equo just fork a shell script to upgrade python which doesn't depend on the python libs? Why is python dying during the upgrade of itself. Somehow portage has been doing it for years without problems.
If you guys fix this, I'll make a network install script I was thinking of for people with linodes and the like.
I've been meaning to do that for a while.