I will start by addressing the specific question that you have asked here: "According to Halacha, is it a sin for a Jew to take control over some land in Eretz Yisrael when this land was taken against the will of its previous controller (regardless of whether it was occupied or empty, and whether there was violence involved in the transition)?"
The answer to your basic question is, "no, there is no general prohibition against taking Eretz Yisrael by force (i.e. with violence)." War is not something that Judaism views as universally forbidden. Indeed, the conquering of the Land from the Canaanites by force was itself a commandment (Deut. 20:16). Your comparisons to theft are not really analogous: stealing is forbidden; conquering land is not forbidden. Therefore, there is at least one case where it is not a sin to take control of some land in Israel by force.
Of course, the conquering of the Land of Israel from the Seven Nations who were living there was a special case and not necessarily directly relevant to today. You mention that the motivation for your question is understanding the halachic issues regarding Jews nowadays moving into land previously controlled by non-Jews in Israel.
Your suggestion in the question was that perhaps this is a violation of the prohibition against stealing. It turns out that this actually cannot be the case because of a halachic technicality called קרקע אינה נגזלת ("land is not stolen"). This should not be understood as a permission to steal land; rather, it should be understood as a technical description of a scenario. In short, land that is taken from someone against his will is not considered to be "stolen" but rather still in the domain of the original owner. It is not necessary to completely understand this distinction for our discussion here; what is important is that the technical halachic prohibition against stealing cannot apply to land. (If you are interested in learning more about this halachic concept, see the Gemara at Sukkah 30a-b and Bava Kama 117b).
All this tells us, though, is that taking someone's land against his will is not called stealing. That doesn't mean that it is permitted. In fact, Shulchan Arukh 376:1 rules that trespassing is forbidden and compares it to stealing. So the question here is, are Jews living in Judea and Samaria trespassing on the land of non-Jews?
Unfortunately, this is the point in our discussion where the answer depends on whose version of the facts you accept as true. The State of Israel claims that its wars have always been wars of self-defense and any land captured has always been taken for strategic reasons related to national security. Wars of self-defense are permitted according to halacha. Moreover, many Israel supporters also claim that Arabs were never (or at least only in isolated instances) expelled from their homes. They claim that those who left did so voluntarily with the encouragement of Arab leaders who told the public that after a swift destruction of Israel, they would be able to return. If you accept this version of reality, all of the land controlled by the State of Israel was legally captured in a legitimate war and the Arabs who had been living there abandoned their land anyway!
On the other hand, someone who rejects this version of the facts could possibly come to a completely different halachic conclusion. That is part of the reason why there was so much resistance to your question in its original formulation. The original question was a question about the facts on the ground in Israel. We do not answer that kind of question on Mi Yodeya. Here, we can only answer questions where the scenario is well-defined and the question is about Judaism.