Of course, they likely would have had a warrant, and if not, might possibly have gotten one from the FISA court (I'm not sure on the process there) which pretty much always issues a warrant, so it still wouldn't have been great for him.
In this case, I suspect there are federal laws against shooting FBI agents, which would trump state law.
Even if there weren't, well, suspects aren't always taken alive to be vindicated in court.
I don't otherwise disagree with the synopsis you've put forth, I'm just saying that our right to bear doesn't prohibit us from ever firing in the event that there is clear justification. People storming your home is such a justification, no matter what uniforms they're wearing.
Fun fact: Timothy McVeigh was convicted of the murder of 8 federal agents who were in the Federal Building. They didn't bother to charge him with the other 160 counts of murder, because those weren't federal crimes.
If I kill someone attacking me, I have committed homicide, but not necessarily murder. If I kill someone ala McVeigh, I have murdered them.
Since it is a federal charge, it's very likely that the 'intent' would be determined in a federal court, which does exist outside of state jurisdiction and is bound to uphold federal laws, but it isn't quite open and shut.
Still, your point stands, which is to say that he's almost certainly screwed.
What we really have in this country is literally a "right to bear arms". You have no right to fire or wield or use your arms.
I can think of no situation where you could fire upon an agent of the government that would not end badly for you, unless there was a total dissolution of Federal and probably State government. Even acting in self defense, even against a corrupt agent of the government, I can't imagine it ending any way but badly for you. You can't shoot the government a little to make a small change. Either you completely overthrow the government, so that there is no one left to hang you, or you go to jail in the best case, and be executed lawfully or gunned down in the street in the worst case.