Rufus is a bad guy. He is in opposition to your side therefore he is the enemy. Here is my counter to everything you said.

1) Not for the people but for himself. He wants power and you can't have anything if there is no world to control.

2) How does this not make him a bad guy?

3) Weapon is a danger to his power and control of the people. Defeat something like that and the people will love you. Let it destory everything and people will lose trust in your ability to protect them. It also serves as a deterrent for those who would oppose him.

4) And everything he just got! Sure the people would die but then there is no power or control over anything. Gotta try to stop it or else you lose it all.

5 & 6) I don't remember the fight too well. But he fled so that he didn't lose or else there goes all his ambition to gain control of EVERYTHING.

7) Didn't you just describe hitler's way of contolling people? Hitler didn't hurt his own people. They worked for him and he did his damnest to protect them. Thats why they all followed him. Sounds like Rufus to me.

8) Rufus controls Heidegger. Why would Heidegger even tell them to find cloud with out hearing it from Rufus. Its not like Heidegger has really run into cloud and the gang by that point. But Rufus has. Rufus is a busy man and can't tell every person every thing. Pass it off to someone and tell them to 'Deal with the problem'

9) I am sure his objective with that big cannon was to kill cloud in the most horrific way possible...pffffft. It was to try and kill sephiroth so that he could control the world. Sephiroth would control the world if he couldn't kill him. Its just another power struggle.