Yes the performance impact of a single "alert()" when i open the page is negligible. The performance impact of parsing Markdown and rendering it as HTML nodes is definitely non-negligible.
I love the idea to support more markdown formats natively for the web (eg. markdown), but i hate client-side scripting shenanigans that don't respect me as a user without the fancy latest iphone. If only some browsers were concerned about emerging protocols/formats & UX instead of increasingly-useless (except for tracking purposes) JS APIs...