That assumes she's showing empathy with the enemy and now questions their own actions morality. I don't think that is the case though,
In fact, that kind of question - and its timing especially - feels so very very whisper. It's probably important to realize she is most probably not morally accusing anyone of being bad in making the first hostile move, she's simply trying to find a logical explanation why everyone's acting hostile to them all the time.
I guess most captains would have interpreted that question as moral critique in their leadership. But Ward knows Whisper well enough, so he simply makes it clear he doesn't have time and nerve to deal with that kinda crap in the midst of battle.
But, assume for a second, Ward had answered "Yes, that's probably why." What would have been Whispers response?
My bet is, Whisper would simply have smiled, nodded (mystery solved), and continued managing Niobe's system for optimum weapon efficiency, so they can continue dealing hostilities to the enemy and finish them off.
Daniel... Daniel assumes actions are inherently "good" or "bad" based on motive on moral principles. I'm not quite sure Whisper really gets that concept. For her "good" actions are actions that will have positive long term repercussions for her, while "bad" actions are those that will eventually backfire.
There is a lot of overlap between those definitions, but for Whisper, whether shooting at a 3rd party is "good" or "bad" simply depends whether the aggression is more likely to cause the opponent into future retaliation - or intimidate them to cease hostilities altogether.
From that point of view, there's absolutely nothing wrong with "make no prisoners, leave no survivors, only an expanding cloud of plasma" - expanding plasma doesn't hold grudges, nor does it remember who took the first shot, as thus there's rarely ever any problematic consequences.
Leaving certain pirates alive however led to "complications". But of course showing mercy can have social benefits in the long run. Its always a trade-off, which she's willing to make -- especially since it makes Daniel happy. After all, that's also a positive consequence.
I guess, she totally will let her enemies live if it makes Daniel smile.