Taking your two examples--chemical weapons designed to create fear among survivors could diminish potential resistance bloodshed in a situation where the invader was committed to winning and had the resources to do so but chose an easier path. This could, then, be seen as a lesser evil (to bombing a nationalist resistance movement into the ground before entering an area). Biological weapons (yes, I know you are likely referring to the "bad kind") could be used to give everyone debilitating weakness ... thirst, you name it, in order to allow for an easier invasion (just make sure the invading troops are inoculated). Some would die from complications in all likelihood but less than if bombing / tanks / etc. had to be used.
In both my above examples, I am positing a set of weapons that cause no long term harm to the populace yet still fall into your categories. Even if there is long term harm (perhaps no one in the invaded country can handle a jack hammer for ten years or something), we still have an improvement over widespread bloodshed (but this does present the issue of what "improvement" is). If we are talking a serious weapon that causes permanent nerve damage or wipes out an entire population like a type of weaponized small pox might, this is still going to prevent infrastructure damage and allow for a faster local recovery among survivors / immigrants. Hiroshima was bad as was the more widespread bombing of Japan by conventional weapons. If Hiroshima had been left standing but all the people who died killed directly (still horrible, but we are talking about war), then the recovery could have been accomplished in a matter of weeks instead of years.
Some of the above may be distasteful--I wouldn't want to go to the lengths indicated, but the tools are simply tools. The weapons aren't evil--their application by human agents could be depending on the situation and the strength of dose, etc. It still boils down to humans standing at the root of the problem, not the mechanisms. Blaming machines (which is what it could lead to) will only exacerbate existing problems.