Regards to nuking a planet;
Yeah, it's not something most humans would want, especially if they're going to be living on it afterwards. However, there are some very serious implications to planetary conquest, especially in the Sins universe.
The most noticeable is that conquering a city requires enormous amounts of power and numbers, nevermind a country, or furthermore an entire planet. Even Lucas said that he kind of chickened out with the immeasurable amount of resources required for planetary conquest in Star Wars. You would need millions upon millions, if not billions to be able to conquer a planet and hold it. This is one of the things GalCiv did right, and that was transport ships had billions of soldiers in them.
This presents a problem for any civilization that just doesn't have a hundred billion citizens that can support and maintain a conquest strategy on a conventional scale. The time and effort spent would be an undertaking comparable with that of the entire history of human civilization.
Even in Sins, the technology is just not there for that kid of conquest. The military forces of all of the factions are primarily naval based, with the vast majority of personnel being either shipmates or support. The type of warfare that takes place in Sins is primarily naval engagements between starships, and with the huge amount of vessels that populate their galaxy, most bodies are dedicated for ship-to-ship combat and the support elements behind that type of warfare. This is further seen in how planetary conquest is conducted in sins (nuking a planet)- the side with the strongest and largest fleet of starships wins. There is virtually no army that we know of other than marine and planetary police forces. And those hardly, if ever play a role in the war doctrines of Sins.
Even for the Advent, it would be otherwise impossible without tarnishing their own morals with that of planetary genocide. Converting even a majority of the population presents you with the same problem- you still have to win the battle on the ground against those that won't convert. This can take a hundred years for a country, it mostly likely will never cease with an entire planet, especially considering the elements that come with insurgency and renewed rebellions. The only way to ensure prolonged conquest or dominance is replacing the population in its entirety, as the inescapable formula of eventuality will eventually bring your attempt at a more humane conquest crumbling down. Something history is most capable of proving time and again.
And for the other factions, its about available resources. They can barely field fleets to maintain a stalemate, they have a hard enough time keeping a capital ship from getting destroyed. If they could even manage to build a large enough invasion force, it might as well be turned defensive as the time, manpower, and raw material required to muster a necessary element would have rendered that faction vulnerable to the enemy who have spent the entire time building capital ships and nukes. In a matter of seconds, that invasion force you've spent decades building up is gone under the rain of nuclear holocaust.
Thus, the only realistically achievable method of conquering a planet is similar to what we see in ancient human history. Complete annihilation of the indigenous population and the expensive, long-winded, and entirely vulnerable recolonization that follows from the victors. It doesn't have to be nuclear, but if any of the factions had a population and economy that could afford 1, 2, 3, 4 or however many billion standing armies supported by even larger numbers in the navies, then Sins of Solar Empire would be an entirely different game. This is why planetary conquest is the most dangerous game a military can play in conventional methods. The bureaucratic establishments that would need to be in place to support a system or galaxy-wide strategy would be on par with the size of the 40k or Star Wars Universe, and in 40k planets are never fully conquered even with their billions of casualties per world, and in Star Wars the consequences and strategies are very rarely touched upon (to which Lucas even admits the almost unimaginable scale of it).