There were a few factors that led to the war.
Halo Encyclopedia Page 43
“During colonial expansion, Humankind made some [Forerunner] discoveries that were kept as closely guarded secrets by the UNSC’s Officer of Naval Intelligence.”
Halo Encyclopedia Page 43 (continued)
“The complete power that ONI exercised over the control of research and information flow from these various discoveries showed their growing power within the UNSC and the Government’s desire to maintain control over the colonies. As Humanity expanded, the UNSC took every step necessary to keep its grip on the Outer Colonies. The Inner Colonies depended on the resources the Outer Colonies provided and the Outer Colonies depended on UNSC-maintained supply lines. By the 2400s, Outer and even many Inner Colonies soon began to question the often draconian interference of the UNSC in what was supposed to be a confederation of independently governed worlds.”
Halo Encyclopedia Page 44
“As the UNSC increasingly countermanded and complicated the functioning governments of the Inner and Outer colony worlds, unrest began to foment. Complaints were generally ignored by the UNSC until finally rebellion began. Minor uprising were common throughout the settling of the UNSC colonies but the superior forces of the UNSC had been able to put them down easily.”
Halo Evolutions Page 428 - 429
“It was the end of the Golden Age of human colonization. As of 2494 CE it was still a time of peace and prosperity, but Earth had begun to overreach its logistical ability to control her colonies. Several factors led to the destabilization of the more distant, or as later called, ‘Outer’ Colonies.
1. There were widely varying standards for recruitment to the Outer Colonies. ‘Colonization contractors’ were more interested in staking claims to valuable resource rights than providing the most-skilled personnel. Some people were illegally conscripted and others were law-breakers granted pardons if they agreed to go-all of which led to these colonists being less than absolutely loyal to Earth.
2. Some colonies struck out on their own, procuring by legal or illegal means of transport to farther-flung worlds, partially or wholly outside Earth’s control.
3. Continued taxes, levies and restricted trade practices by the CMA increased friction as the Outer Colonies received only a fraction of the benefits they were taxed for.
The situation was a problem of physical as well as psychological dimensions. Mathematically the volume of the sphere increases as its radius cubed and so the number of Outer Colonies grew. Given such a numerical advantage and the fact that they encapsulated the Inner Core worlds, there was the belief that Earth and her close colonies were literally surrounded by increasingly hostile forces.
Many now think this was a skewed perception and that given diplomacy and enough time, Earth and her Inner Colonies could have established more harmonious relationships with her farther-flung cousins. Others point out, however, that had there been no military action, the Outer Colonies might have risen to power and threatened the core worlds at the worst possible moment in human history.
All theoretical analysis aside, the United Earth Government and her colonies developed new policies and an increased military presence that would provoke further unfortunate responses from the Outer Colonies… and lead to an undeclared Civil War.”
So we have colonies that were made up of illegally conscripted workers and criminals the UNSC simply wanted out of their sight. This ends up establishing groups of people who didn’t really have any true loyalty to Earth to begin with. Then as they began to build new homes for themselves, they discover Forerunner structures which then piques the interest of the Office of Naval Intelligence. In order to ensure their dominance over these extraterrestrial discoveries the UNSC tightens its grip over the colonies and when they protest the UNSC simply increases their military presence even further.
The UNSC interferes with the way the colonies are independently governed, The CMA begins to overtax them which diminishes their ability to make a living and when they protest the UNSC ignores them. This ultimately causes outrage and eventually secession, such as the colony world of Far Isle. When the UNSC couldn’t bring the population under control, they nuked the colony. There were no survivors.
It would seem it was all one big gamble. The UNSC could have done more to find a more peaceful solution but not everyone agreed. They knew either way based on the Carver Findings something had to be done and in the end they chose to go with the military option. There is no way of knowing for sure if the peaceful solution was the better option, but I personally think it would have been preferable to nuking your colonies to death.