Wordpress - How to display non-hierarchical taxonomy as terms with checkboxes?
I got the solution (based on the tutsplus tutorial link above) that deals with actual checkboxes here to work: http://wordpress.org/support/topic/display-tag-admin-box-like-categories-without-hierarchy it ignores the "most used" tab of the metabox that the tutsplus link addresses but personally I'm keeping it simple.
I'm not sure, if you already found a solution for this, but when I searched for a similar one yesterday, I found this tutorial on WPtuts very helpful. It uses radio buttons, but you can easily modify it to get it working with checkboxes as well. http://wp.tutsplus.com/tutorials/creative-coding/how-to-use-radio-buttons-with-taxonomies/
Pardon my french, but why not use the built in hierarchial=true and after that hide all the Parent dropboxes by using admin css ?