Spoilers?
They weren't subtle at all.
The crews of the Pegasus and the Galactica have been taught the first lesson of war. Dehumanize your enemy. Call them "toasters," deny their rights as sentient beings, and whatever you do them (and your own people) in the name of victory is not only acceptable, it is to be commended. However, don't get caught. Don't be visible to the public. Don't let anyone outside of the chain of command question any decision.
On board the Galactica, the crew is answerable to a civilian government with a press that scrutinizes their every move. They are part of a fleet. They are forced to make decisions based on the needs of the many. Team work and community sacrifice keep the unit functioning in the face of overwhelming odds. They make mistakes. They learn from them and press on.
The Pegasus has no check and balance against corruption. They are one ship. It is lead by higher ranking officers of great repute. Their word is considered law. Rules are not meant to be broken. No dissent is allowed. Indeed, it is cut out immediately. Propaganda, esprit de corps tactics and fear are used to keep the troops in line. Torture of prisoners is allowed, even encouraged. The units are successful, but at what cost?
When these two elements collide, which is more acceptable? Which will the "public" stomach?