Yes, CPU usage is a minor concern. But there are ways to make it not such a big deal.
The specific case that Vautrin seems to be talking about is when somebody has a big block of Perl code that they have pasted into code blocks. In those cases, it can be hard to follow for those of us who have been spoiled with syntax highlighting. I don't think that means that all code blocks need to be highlighted all the time.
As multiple others have already suggested, if there was a link, similar to the download code link, that was basically a "View code with context markup", then the monks could use that link whenever they wanted to, but otherwise it would take up no more CPU than normal. This also solves the "not all code blocks are Perl" issue.