But that plugin system also is one of WordPress' greatest assets. And you can add PHP code to any part of a "theme" too. If you turned off the ability for themes and plugins to be "added live" then I don't think WordPress would be nearly as successful as it has become.
Wordpress is not PHP.
And I think you can definitely argue that a low barrier to entry means that it gives beginners a lot of power they don't quite understand.
Which is why I think most people steer towards common web frameworks, because not many people can know all the ways you can create security issues.
Then you get into the complexities of various common web frameworks (Zend, etc) and you have to really wonder if the original OPs argument about simplicity and ease-of-use are worth that trade-off from using something else.
Perhaps end-users should not have the capacity to so easily add third party PHP code, even if it’s “simple.”