This is really one of the biggest issues I have with the plot in the second disc (well not to mention that stupid double whammy plot twist about Cloud) cause while Shin-Ra is certainly only fighting for their own self-preservation and they were certainly the main cause of all this from happening, like Crop points out, it's not like Cloud's party actually had a plan. The truth about Holy doesn't even come to light until after Cloud and co. have sabotaged Shin-Ra's efforts to save the planet. So they pretty much wasted time of figuring out their own way of saving the Planet by screwing with Shin-Ra's plan which at the time could have been the planet's only hope.

They really had no good reason to do so beyond some hippie environmentalist mentality The game does a piss poor job of explaining why the heroes are in the right, nor does it really give any literary focus of presenting the heroes as not completely good, they simply come across as stupid and their justification is that Shin-Ra is evil. I'm guessing something was lost in translation but I don't really care anymore.