.htaccess for Craft CMS - removing segment from URL
I might be way off here, but if you are wanting to run Craft as your main front-end, could you not place the Craft index.php in the root of the site and then you CRM in a sub-folder of its own?

If you have all you CRM stuff in its own sub-folder, Craft should just ignore that folder as it physically exists. If you've got specific things you need to have in your .htaccess file for you CRM, you could have that .htaccess in the sub-folder, rather than the root. That way you can just have the standard Craft .htaccess file in the root of the site.