I didn't say they wouldn't do it... I just said they would think about it, and perhaps try not to.
In a kill-or-be-killed situation, yes... you would shoot to save yourself. The guilt comes later.
When planning to takedown the enemy... if you know there are unwilling participants, you might try a different strategy.
In the real world, for example, our troops drop fliers and food and things into hot zones hoping that if the people see that we don't hate all of them... some might not fight us, so we can get to the ones in charge easier.
In this show... IF they now know the Skitters are enslaved in a similar way as their own children... they might consider a path that leads them to a new ally in the war. Instead of killing the Skitters... they now know there is a bigger/badder enemy that they need to take down... and IF they found a way to set the Skitters free, perhaps they have more allies to win the war against the real enemy.
IF you don't at least consider that... you'd be a fool. You might waste time and ammo killing Skitters that could have been an ally to you... and still you haven't actually made a dent in the actual enemy alien.
It just seems to me that smart strategy would be to make allies with someone (or something) that has a common enemy and your chances of success are higher.
When they thought the Skitters were in charge, it made sense to attack them... but knowing they are the grunts... it makes less sense. In a war you do have to take out whomever is in your way, but your target is the bigger fish.