Right. But there is a difference between casualties that occur in the line of duty vs those that occur in pursuit of a personal task.
That's the thing - let's go with the assumption that SHIELD agents sometimes need to do legally and morally gray things in the pursuit of a higher cause, or have the authority to bypass normal legal procedures and requirements in order to get the job done. That the stakes are high enough that it justifies operating outside of the normal domain of the law.
It is a completely different thing to do so while on the job vs doing so for personal reasons. And, ultimately, that is what was happening here.
If a cop's wife is dying, and he breaks into a hospital to steal medicine for her, and there is a security guard who fights back against the armed intruder, and the security guard is killed in the ensuing gunfight... the cop's badge doesn't excuse his actions. Nor the fact that he asked nicely before then forcefully breaking into the hospital with weapons at the ready.