If you are referring to the Geass cult, it does not matter whether they were unarmed or not. They were dangerous, and any mercy shown would have resulted in defeat via Geass.
Suzaku is betraying his principles by doing this. Also he is being a bit of an asshole by using a drug he knows is highly addictive and one that virtually ruined Kallen's mothers life. Even if he doesn't know about Kallen's mom, he should know better than to use an addictive substance.
Most of the rage comes from the fact that this is an act is the result of a gut instinct on the part of Suzaku with no definite proof. Granted, his gut instinct is partially on target, but what he is doing is not proportional to what he knows so far.