Right then.
The Federation as a whole, is a representative democracy, in which the voters elect representatives, and then it is the representatives that make governmental decisions. It is not a direct democracy where the voters decide policy directly. There are some sub-polities within the Federation which are direct democracies, where the citizens vote on issues of the day, and then officials conduct policy accordingly, but the Federation as a whole is not like that.
You have the President, who is elected by a popular vote across the Federation, and the Senators, who are representatives elected by a vote in the areas that they ostensibly represent.
The President attempts to implement their agenda, various senators attempt to implement theirs. On a rare occasion, these agendas are what the people of the Federation as a whole would actually approve of.
The election process is somewhat flawed, because essentially, it is asking billions of people which candidate they want as Senator. Trillions in the case of the President. Getting such large numbers of people to agree on anything is extremely difficult, and there is a great deal of dumbing down and lack of nuance in political media coverage, in order to force a decisive result.
So in a substantial amount of the time, the candidate that is elected, their views are not quite what the people thought they were. A candidate might express the position that they would “strengthen society”, what does that even mean ? They get elected, and only then do the population find out what they meant by such vague positional statements.
Now then, if we look at alleged crimes committed by Federal forces, we see that above a certain operational command level, appointments are political, rather than strictly on merit. Senior Admirals, Generals, etc. are appointed with the approval of the President and Senate, and thus it is the Senate and President that bear responsibility for any crimes committed under orders from the politically appointed officers. While the population elects the Senators and President, they do not appoint the high command, and thus, bear no responsibility.
Of course, some crimes will be committed without the knowledge or approval of high command, in that case, the guilt lies with the officers issuing the orders, and not with the population.
So we see that the general population of the Federation, is not directly responsible for the crimes that may have occurred. In a lot of cases, the population did not vote for the senators or the President that made the decisions that facilitated those crimes occurring, and thus, cannot be held responsible.
So, no, you’re not going to take trillions of Federal citizens prisoner. That’s just silly.
As for dealing with the Imperial authorities. They don’t have the facilities to absorb trillions of new subjects, who would all then need housed, clothed, and fed. Which would compel the Empire to annex a lot of systems, to provide those basic needs to their subjects.
And for the legal position - no Caldari officer, in good standing or not, has the authority to traffic in slaves within the Empire. That would be acting as an illegal slaver, and that is something the Imperial authorities take very seriously. Only appropriately certified and licensed slave traders are allowed to operate within the Empire’s jurisdiction.
SO, to answer your questions:
“Does this also mean that every Federal Citizen is complicit in crimes that the Federal Government has committed ?”
No. Those committing the crimes, those ordering the crimes, and those who appointed them to the positions, are complicit. Not the general citizenry.
“Shall we treat Federal Citizens as ones who are responsible for deaths caused by Malkalen Incident et.al. ?”
No. Same reasons as above.
“Would it be ethical to source captured Federal prisoners (including citizens) to the Amarr Empire ?”
No.
“Would the Empire consider them criminal as well ?”
No.
I hope this response was informative.