Regarding the Dehaan affair. What I know about it is from Guardian of Jerusalem, the Artscroll biography of Reb Yosef Chaim Sonnenfeld ZTL. Even in a book obviously written from an anti-zionist perspective, you can clearly see that he was very possibly a mored bmalchus and a traitor and would have sabotaged the entire state.
While the Zionist leaders were going around the world speaking with all kinds of dignitaries and governments trying to get a state set up and making all the zillions of arrangements that needed to be made (remember my mashal about the shul dinner multiplied by 10 million for the difficulty in creating a state), Dehaan was about to go abroad and tell certain govts that they should not pay attention to the Zionist representatives. He could literally have destroyed any chance for getting recognition and assistance.
I am not saying one way or another whether the murder was halachically correct (if in fact it was committed by Jews), but you can certainly see how he was a thorn in their eyes, and how serious a threat his meddling was.
Regarding the Altalena, I always thought the since Yitzchak Rabin was (I believe) one of those who fired on the ship of fellow Jews, midah kneged midah, he was murdered by a fellow Jew. However, I now understand better why this happened. Before the state, the Haganah and Irgun and other groups all were fighting the British in their own ways. It was like the wild west with no chain of command. However, once the state was set up, it was agreed that there would be one Tzahal and everybody would follow orders and subordinate themselves to the Tzahal. However, this ship was bringing in private heavy weapons to one of the groups (Irgun?) and they were planning to do whatever they felt like with those arms and not necessarily follow orders from the new IDF.
This was intolerable to the Haganah that it would be a free-for-all, without discipline, so they sank the ship to show that now there were rules for weapons. (I am not justifying this, just presenting the rationale.)
Lhavdil elef havdalos, it might be roughly like the situation in Lebanon, where Hezbollah has their own private arms and rockets, totally separate from the Lebanese army. They on their own started the second Lebanon war in 2006. One cannot have a state within a state without causing chaos. Again, I am not saying what was right, as I was not there and am not a historian, I am just presenting a point of view.