If this can be implemented so that the highlighting happens after a node has been created/edited, and the result can be cached as HTML, the impact on the site's performance should be neglectible.
I would like to recommend to let the author decide whether or not a piece of code should be highlighted (i.e. not make it configurable in the User Settings). The reason is that syntax highlighting tools are not always perfect. Sometimes highlighting makes the code look really bad. (Moreover, <code> tags don't always contain Perl code.) If the author notices that, they can choose to either reformat the code or disable the highlighting.