Oh good topic that is open to a bunch of wild guessing and speculation.
I'm not sure if this is directly related, but from
Inzil's thread there was discussion about the plague Melkor sent and then the one in the Third Age.
Melkor is totally the type of villain that would send a plague to his enemies, but also wouldn't care how it would effect his own designs. As we know Tolkien refers to him as a nihilist and he wouldn't care if the "Evil Breath" killed his own. But was Sauron?
Well, he wasn't a nihilist, but what I do like about him (as a villain in a book) is he thinks and acts as an immortal. Too many fantasy authors create immortal villains but don't necessarily act like one, Sauron does. He's quite patient, as in Numenor and then when he returns in the Third Age.
I believe the date given is circa 1100 that an evil power inhabited Dol Guldur. Sauron spends thousands of years weakening resistance to reach his end goal. He acts like an immortal villain, patient and plays the long game. So, while I don't think Sauron liked being wasteful with resources (like Melkor was) if he did send the plague that also effected his own troops it could be in his calculations that's an acceptable loss for his long-term designs, if his goal at the time was to get Gondor out of Mordor, as well as depopulate Eriador.