I would like to point out that Cayleb and Sharleyan have already rejected the use of terror, for example Ferayd, and the rejection of the Book of Schueler, other than the immediate execution of any member of the inquisition captured, so I doubt that they would countenance any use of biological or indiscriminate weapons.
Well, with the help of Merlin, they could afford it. But what if they haven't Merlin's help? Or the other side have their own equivalent? Would they still be so "nice and civilized", even if it means that they clearly would lose (with disastrous consequenses for their populations), or would they throw against Clyntahn everuthing they could obtain - gases, viruses, radiological bomb?
The fact is, that in real total wars, there is no Merlins or Mary-Sue or anything like that. There is two powers, struggling against each other with all they could manage.