Except at the time they weren't "innocent beings", they were "hideous alien monsters". Doctor Who has many examples of people doing things to aliens which would probably be considered war crimes if they'd been done to humans. The Brigadier blowing up the Silurians for example.
The Silurians was akin to the Bombing of Hiroshima, a necessary war crime, they had (after all) just tried to exterminate humanity. Chrmical Warfare is never justified. Because it's indiscriminate.
Post-Day of the Doctor, which is when Harry made the gas, the Zygons were refugees.
There was nothing necessary about bombing the Silurians. They had already gone back to sleep when the Brigadier blew them up. The ones resonsible for the virus were already dead. Most of the Silurians who were blown up were asleep throughout the episode, and didn't even know about the apes.