Since you are asking a halacha question here and I don't want to wade into politics, I will address 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](http://www.mechon-mamre.org/p/pt/pt0520.htm#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.