The Marcuses work to change the world, by changing worlds. It's not exactly a "preservation" philosophy. Plus, they are in the business of creating potential for life, so what's the point of worrying about loss of such potential in Genesis detonations? There's no loss!
Yes, there is. As Spock said later, if there is life on a planet that Genesis is used on that life would be destroyed in favor of the new matrix. The purpose of Genesis was to transform lifeless planets. There is no contradiction between Marcus wanting to create new biospheres out of lifeless planets and a desire to not interfere with life (or potential life) that already exists.
"Canon is only important to certain people because they have to cling to their knowledge of the minutiae. Open your mind! Be a Star Trek fan and open your mind and say, 'Where does Star Trek want to take me now'." - Leonard Nimoy