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.
Correct. The potential for either outcome exists, but which outcome ultimately manifests itself is dependent upon the decisions and actions of whomever controls the device.