Yes, I believe that's the theory. Materia form when Mako energy condenses and crystallises. However, Mako energy is the life energy, the essence of every living thing. Materia form naturally, in caves and springs like those seen in the game; this is a natural process and the crystals don't remain forever, they return to their natural state. However, Shinra's Mako reactors are used to manufacture Materia artificially, outside of the natural cycles. Every time a Materia forms, there's a little less spirit energy in circulation. In theory, if enough Mako was processed into Materia, life would start to diminish - the same as what happens around Mako reactors themselves. So, to have and use Materia is to contribute to the problem, at least in a small way... but at least it's possible to return Materia to the Planet when you're done with them. This is mentioned in the Materia tutorial - "If you've got too many, you can always throw some away - I mean, return it to the Planet".