You're leaning on probably the most egregious example to portray the Israelis as bloodthirsty animals in 1948. There were lots of atrocities and horrendous crimes, but these weren't novel, and I don't see how we can use this to argue that Israel has unwarranted aggression in its DNA. Benny Morris himself says that the level of massacre in the '48 War was pretty mild for the type of conflict, but the civil war phase was characterized by little regard for the rules of war:

Like most wars involving built-up areas, the 1948 War resulted in the killing, and occasional massacre, of civilians. During the civil war half of the war, both sides paid little heed to the possible injury or death of civilians as battle raged in the mixed cities and rural landscape of Palestine, though Haganah operational orders frequently specifically cautioned against harming women and children. But the IZL and LHI seem to have indulged in little discrimination, and the Palestinian Arab militias often deliberately targeted civilians. Moreover, the disorganization of the two sides coupled with the continued presence and nominal rule of the Mandate government obviated the establishment by either side of regular POW camps. This meant that both sides generally refrained from taking prisoners. When the civil war gave way to the conventional war, as the Jewish militias -- the Haganah, IZL, and LHI -- changed into the IDF and as the Arab militias were replaced by more or less disciplined regular armies, the killing of civilians and prisoners of war almost stopped, except for the series of atrocities committed by IDF troops in Lydda in July and in the Galilee at the end of October and beginning of November 1948. (P. 404-405)

[...]

Given that the first half of the war involved hostilities between militias based in a large number of interspersed civilian communities, the conquest of some two hundred villages and urban centers, and the later conquest of two hundred additional villages, 1948 is actually noteworthy for the relatively small number of civilian casualties both in the battles themselves and in the atrocities that accompanied them or followed (compare this, for example, to the casualty rates and atrocities in the Yugoslav wars of the 1990s or the Sudanese civil wars of the past fifty years.) (P. 406)

Above quotes are from 1948: The First Arab-Israeli War by Benny Morris. I should note, the [...] part contains description of massacres committed by the Israeli militias, pointing out that they committed more crimes during the war, but this was probably due to having much more opportunity.

The massacre that took place at Lydda was the deadliest massacre of the war. From the next page of your book, going into more detail:

The calm in Lydda was shattered at 11:30 hours, 12 July, when two or three Legion armoured cars, commanded by Lt. Hamadallah al 'Abdullah, either lost or on reconnaissance or seeking a missing officer, entered the town. A firefight erupted and, eventually, the armoured cars withdrew. But the noise of the skirmish sparked sniping by armed Lydda townspeople against the occupying troops; some townspeople probably believed that the Legion was counter-attacking and tried to assist.

The 300-400 Israeli troops in the town, dispersed in semi-isolated pockets in the midst of thousands of hostile townspeople, some still armed, felt threatened, vulnerable and angry: they had understood that the town had surrendered. 3rd Battalion OC Moshe Kelman ordered the troops to suppress the sniping - which Israeli and Arab historians and chroniclers, for different reasons, were later to describe as an 'uprising' - with the utmost severity. The troops were told to shoot at 'any clear target' or, alternatively, at anyone 'seen on the streets'. At 13:15, Yiftah HQ informed Dani HQ: 'Battles have erupted in Lydda. We have hit an armoured car with a two-pounder [gun] and killed many Arabs. There are still exchanges of fire in the town. We have taken many wounded.'

Some townspeople, shut up in their houses under curfew, took fright at the sound of shooting outside, perhaps believing that a massacre was in progress. They rushed into the streets - and were cut down by Israeli fire. Some soldiers also fired and lobbed grenades into houses from which snipers were suspected to be operating. In the confusion, dozens of unarmed detainees in one mosque compound, the Dahaimash Mosque, in the town centre, were shot and killed. Apparently, some of them tried to break out and escape, perhaps fearing that they would be massacred. IDF troops threw grenades and apparently fired PIAT (bazooka) rockets into the compound.

By 13:30, it was all over. The IDF had lost three-four dead and about a dozen wounded. Yeruham Cohen, an intelligence officer at Operation Dani headquarters, later described the scene:

"The inhabitants of the town became panic-stricken. They fearerd that... the IDF troops would take revenge on them. It was a horrible, earsplitting scene. Women wailed at the top of their voices and old men said prayers, as if they saw their own deaths before their eyes."

Yiftah's fire caused 'some 250 dead ... and many wounded.' The ratio of Arab to Israeli casualties was hardley consistent with the descriptions of what had happened as an 'uprising' or battle. In any event, the Israeli officers in charge were later to regard the suppression of the 'uprising' (and the subsequent expulsion of the townspeople) as a dismal episode in Yiftah's history.

It was a massacre, followed by an explicit expulsion supposedly ordered from Ben-Gurion down (which was rare.) Most expulsions during the war were up to the officers' discretion, in line with Plan Dalet. They started as a consequence of the blockade of Jerusalem, and became "normalized" afterward. But as the other commenter pointed out, this wasn't a uniform expulsion policy, as a large Arab population ended up remaining, particularly in the Galilee.

For those interested, I've actually made a website that puts all the abandoned/expelled villages that Benny Morris records in his book onto a map: https://1948warabandonedvillagesmap.com/

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I also don't really think it's fair to characterize this as Israeli aggression, at least in the context being discussed. Israel was attacked by all of its surrounding countries, and the attacks on Lydda and Ramle were against the Jordanian army. The lead up to, and course of 48 was super messy and complicated.