First off, kudos on an awesome framework for including example code into your site.
The issue is that within the shortcode itself, the Go template engine is parsing the string, and it must be escaped.
When passing the regexp as a parameter to a shortcode, our shortcode parser handles that, and the parameters are treated a literal strings that don’t need to be escaped. So, use this:
{{< githubsource clear="(/\*(?sU).*\*/)|(//.*)" >}}