Well, if system installed programs break if you replace /usr/bin/perl with a newer version, consider using an OS that gets it right. An OS that gets this right is Solaris. It also has important system utilies that use perl. However, the perl that comes with the system is installed somewhere (can't remember the exact location, and can't check now, but it's something like /usr/perl5/bin/perl), with /usr/bin/perl being a link to the real location. None of the system utilities use #!/usr/bin/perl, but instead, use the path #!/usr/bin/perl is pointing to. This leaves users the ability to replace /usr/bin/perl with another perl version, without having system utilies breaking.

Now, if only more Linux distros would see the light.