Khalid,
I have a feeling that your response to the site configuration challenge holds within it a possible workaround to the much debated problem of hierarchical menus when using taxonomy in drupal. Here is what you said:
First, I will add a taxonomy vocabulary, then terms under it, For example, Home, Services, About. Can add Demos, Case Studies, ...etc. if needed...Third, go to the theme configuration and add primary and/or secondary links with Home, About, Services, Products, Contact or whatever else you want.
When I first read it, my immediate reaction was that it wouldn't work because drupal doesn't give an index page to a vocabulary (only to the terms), so how would you be correct about using taxonomy terms as primary links which I interpret as the main sections of the site.
I then realised that you meant setting up Home, Services, About etc as terms of a vocabulary. This vocabulary could be called 'Site Navigation' or whatever and as the vocabulary was a level higher and didn't have to be displayed, essentially the terms would become the main sections of the site.
And, as we all know, a taxonomy term has an index page, and can be manipulated in many ways with modules such as taxonomy_context, taxonomy_menu, taxonomy_block and taxonomy_dhtml.
As a non-programmer, this came as a eureka moment for me, although many months ago, someone suggested something similar- using the vocabulary name for the first term of the vocabulary. Somehow, your approach sounds better.