I didn't mean for this to be so long, but it is what it is...
We don't actually see him kill anybody that we know to be FBI agents or agents of any other government agency...
We don't know the affiliation of the assailants on the plane. From the looks of it they were either working for Antonio or they were part of (if not the entire) corrupt FBI team. One (possible) hint is that the first man to attack Miller on the plane tries to inject him, probably with the same drug that Antonio used on June later in the movie. Also, several of them attack with knives... FBI agents, even corrupt agents don't usually use knives.
For one thing, legitimate law enforcement officers (or even corrupt LE officers) easily could and probably would just try to detain Miller in the airport before he even boarded the plane. They have plenty of resources at their disposal. They could overwhelm him with force in a public area and write the entire thing off as a terrorist plot, or whatever they wanted.
The details of the firefight while driving also aren't clear. The shots appear to come from different directions and then Miller shows up on a motorcycle. I think we are intentionally made to think he was the one shooting, but there were several subtle clues that he was not.
The men we do see him shooting later on did not seem to be law enforcement agents. Neither their weapons, nor their behavior. That entire sequence was intentionally hectic and confusing, but if you think about it, Fitzgerald thought that June was working with Miller so Antonio probably did too, either because he was collaborating with Fitzgerald who told him so, or because he came to the same conclusion.
On the other hand, if he was the one firing, June warns the agent siting next to her that a laser sight is being pointed at him and the shooter seems to delay firing. Either way, that agent survives and we find out later that he was not corrupt. Miller knew a lot of what was going on. He could have known this.
Either way, the affiliation of several of the people after Miller/the Zephyr was ambiguous. In a lot of other movies the super honorable good guy disarms or otherwise incapacitates with non-lethal force the other good guys who don't know any better and think hes the bad guy, and we usually get that spoon fed to us. In this movie, whether he does kill other "good guys" or not, is not made clear. We aren't spoon fed anything. In fact, we are pretty well and intentionally confused about the intentions of almost everybody, including Miller, himself for most of it until the end.
Furthermore, even if he did kill agents who were just doing their job, so was he. If he wanted to survive to protect Simon and now June, then the people trying to stop him and most likely kill him probably need to die. Sad but true.
Don't forget that he takes a bullet for Simon at the end... I'm not sure that we should assume that he kills all of those people just to save himself... and then keeps coming back and putting himself in danger just because... well, that wouldn't make sense no matter what reason you come up with.
If you watched the movie and thought that he was the bad guy - or even an antihero (which would be a better description, but still inaccurate) - then you must have missed a lot of the plot or not paid attention or failed to use some pretty straightforward analytical thinking or something...
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