If you want to run jCore on Hiawatha I'm happy to say that you can. My friend Sebastian just did a quick setup of jCore on Hiawatha and the only thing needed to change was the .htaccess file rules for the SEO friendly links.

Hugo (the creator of Hiawatha) was very helpful and helped Sebastian with these changes, so if you want to run jCore on Hiawatha and with SEO friendly links enabled just use the following in your Hiawatha config:

UrlToolkit {
ToolkitID = jCore
RequestURI exists Return
Match /(.*)\?(.*) Rewrite /index.php?path=$1&$2
Match /(.*) Rewrite /index.php?path=$1
}

You can find more about this at the Hiawatha thread:
http://www.hiawatha-webserver.org/forum/topic/676

and also the How-to section of Hiawatha has been updated with these settings added together with other CMS-es so have a look on this too for further information:
http://www.hiawatha-webserver.org/howto/url_rewrite_rules

Many thanks to both Sebastian and Hugo for testing and letting me known!