The point probably is that the huge materia shouldn't be used like this, and it should be protected, but even then it is a poorly done storyline, because of exactly what you said. If they had made it more clear that what Shinra was doing was still bad, albeit with good intentions, like they could have made it obvious that Meteor wouldn't be destroyed this way, and that Shinra are not only fighting a lost cause, they could be doing something wrong unknowingly (like the Meteor could gain power from being near materia, hence why you have to stop Shinra using it, for instance.)
As the way the story stands, it just seems to be "The gifts of the planet must be protected by the evil corporation" which, while the overall storyline of the first part of the game, there's a time and a place for that, and it's not now. Basically, yeah, they should have handled that better.
Also it's strange - Final Fantasy VII is my favorite of the series, but I also think it pales in some places when compared to Final Fantasy VI, Final Fantasy VIII and Final Fantasy X. Basically, FFVII was my first of the series, and it means a lot to me, and I do see where it has a superiority to the other games, at least in my opinion, but I think with the battle system of both FFVIII and FFX (i.e. interactive) and the overall unique characters of all the three games I mentioned (and other FFs), I think it could have been a lot better,
So yeah, the strange part (in case it got buried in my rambling) is that I still find FFVII the best, but think it did some things worse than other FFs