Were Prince Rheagar's wife and infant daughter not murdered by The Mountain, Sandor Clegane? That's why the Martells wanted his head. Jaime Lannister murdered King Aerys Targaryen, who you agree needed to be removed from the throne. (And Jaime's now learning honor.)
From Cersei's perspective, the Starks are a family of meddling honor-bound fools that are attempting to remove her son, and herself, from power. Eddard, with his snooping around into the true father of Cersei's children. Bran, with his Peeping Tom routine.
Cersei and Jaime had their own justification, as public knowledge of their incestual relationship would have doomed them and House Lannister. Personal survival is not a justification?
All Cersei wanted was to see her son take the throne, and rule with the aid of his mother's wisdom. Any opposition to that desire could be seen as no less than evil.
The Starks? Not exactly goody two-shoes themselves. Sure, almost angelic compared to the Lannisters, but the Starks have their own demons. Eddard's honor? Tainted by Jon Snow. Robb's honor?
Where was Robb Stark's honor to House Frey? He was betrothed to a relative of the Late Walder Frey, and what does he do? Robb decides instead to take a Westerling as his bride. Where's the honor in that?
Now, Cersei was systematically murdering (or rather, having them murdered) everyone that was investigating into who the real father of her children was. Jon Arryn, Eddard Stark...we'll never know if she might have got to Stannis as well. She would have rejoiced in killing Tyrion, I'm sure. If Bran hadn't witnessed Jaime and Cersei, and had never been thrown off the wall, there would have been no need for the assassination attempt upon him, which gave the war a big push. Damn Catelyn Stark and her meddling.
Perhaps I was a bit jumpy in saying the whole war would've been prevented, but I think Cersei was cunning and manipulative enough to ensure Eddard had been sent away, where his voice would not be heard, or killed in a manner as discretely as Arryn and Robert. The public beheading? Joffrey was always a little headstrong.
Things would have taken a different path if Bran hadn't looked in the window. Just ask Cersei.