In 1980, Israel officially absorbed East Jerusalem and considers the whole of Jerusalem to be its capital. That's something completely different from what amounts to people migrating from 1 sovereign country to another. That's saying this place is ours. And they have the military presence to prove it.The fact that Israel has taken over East Jerusalem over international objections might be unchangeable but it is be no means morally right. The fact that they have encroached on more of the Palistinian territory is equally if not more reprehensible.
The mere presence of Jews (or even Israeli citizens) on a particular plot of soil is neither morally wrong, nor legally an encroachment on sovereign territory belonging to another, nor an eventual determination of sovereignty (unless you believe that Palestine MUST be Judenrien). The border has not yet been determined. That is the source of the conflict -- determining the border between the State of Israel and the nascent State of Palestine. The whole point of reaching an agreement is to decide which territory will be Palestinian and which will remain Israel.
The sooner the international community recognizes this basic fact and stops with the cry of "but its Palestinian territory" the sooner we will be over the conflict. And the sooner the international community recognizes that neither the existence of Jews in Palestine nor the existence of Arab Muslims or Christians in Israel prevents sovereignty of those States the sooner we will be over the conflict.