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.
In other words, she has a conscience. Not a hard concept for people to grasp, I hope.
Whatever potential a planet may have to harbor life over time just teeters into butterfly-effect debates. Everything you do could have ramifications pro and con in geologic timescales. That's not something most people worry about, otherwise why get up each morning?
They drew the line at existing microbes, which, IMHO, does fall under treehugger territory in my book.