In and of itself thought is not harmfull. As humans, it's only natural for us to think. When thought does not distort truth there is no harm done and as you suggested, in some cases thinking is a very valuable tool.
The various practices are just trying to point out that thoughts used to create and support unnecessary belief structures, make justifications and provide ongoing mental commentary will be a hindrance in realizing our spirituality. A somewhat quiet mind is pretty much a basic requirement to wake up - some empty space is needed.
