> If you don't allow people to install their own packages, they will just download, compile, and install them into their own directory (or run software written in scripting languages that don't require compilation), and now they have an outdated copy sitting in their home directory that's hard to update, and it's hard to find out that they're even doing this without looking.
In in ideal world: yes that would be better, but you are assuming that all software that might be installed through the package manager is regularly updated. What if the user installs something from a dead or dying project? The package might not be out of date (because no new release is forthcoming), but the sysadmin still needs to know enough about the program to know if it is a security risk.
Requiring explicit permission from root to install anything ensures that anyone who circumvents root's authority to approve/deny software installs is clearly doing something wrong. If its too urgent to bring through normal approval channels and they screw up the install and leave a security whole, then you can fire them. If they aren't confident that the tools they want to install are safe then they can do it the slow way with approved tools.
> Why is it so threatening for users to be able to run their own software? They will do it anyhow
Part of the problem is that you and I are talking about us. We know how to ./configure --prefix=...; make; make install; so WE can circumvent the policy, but WE are also fairly capable of recognizing good safe software from bad unsafe software, WE try to keep track of what we are doing, WE remove stuff we don't need, WE keep our software up to date, and WE appreciate having a tool to automate that process.
I'm not concerned about us, I'm concerned about THEM. The THEM who don't know a phishing scam from a real email, the THEM who think ftp is secure. I don't want THEM installing software. I want THEM to bring a use case forward, and a candidate application for installation so that people like us can guide them in finding the best supported way of accomplishing their goals.