I doubt that the NTF started peacefully, "Vasuadans are teh suck" was a major plank of their platform. They're also fond of attacking civilians, though that was some time into the war.
But a) Bosch doesn't hate Vasudans and b) he mourned the fact that he would be remembered as a butcher of "innocents".
My feeling is that the NTF was comprised of three distinct segments:
1) Those who were disillusioned/dissatisfied with the GTVA and wanted to make a new start
2) Those who simply hated the Vasudans
3) Those who wanted to ally with the Shivans
Number 1 was made up of the Lost Generation (the largest segment, as it potentially includes every single Terran pilot in the GTVA). Number 2 could be made up of just about anybody but probably consisted mostly of line officers who were pilots during the Terran-Vasudan War and still carried around repressed hatred from way back then. Number 3 was likely made up of only Bosch and a very few people in his inner circle. All three segments' goals were different, but the NTF provided a way for them to all overlap.
You can probably compare it to the American Civil War, as the majority of people wanted to simply be left alone to live their own way of life (#1) but there were quite a few very vocal people who tried to make it an issue over slavery (#2). And the North (GTVA) used the pretext of fighting to abolish slavery (racism against Vasudans) as an excuse to tighten control over the rebelling government. Note that neither the Confederacy nor the NTF wanted to overthrow the US/GTVA; they merely wanted to secede and become independent.
The only different element in FS2 was #3. Bosch probably saw that there was a lot of restlessness in the Lost Generation and a lot of leftover hatred from the T-V war, saw that it would probably lead to a civil war eventually, and decided to hijack the whole thing so he could have a vehicle (no pun intended) for accomplishing his vision.