I've read before and re-read just now the quoted military intelligence document. I do not have the complete Morris paper, but I have the book he wrote right after that paper to expand on the research, The Birth of the Palestinian Refugee Problem 1947-1949.
I reread ch 3 of the book after reading this post.
Both describe the migrations as four waves(Morris) or phases(MI report).
By Haganah operations, they do not mean Haganah troops opened fire on Palestine Arabs and move them at gunpoint. They mean that seeing military movements, troops transition from location to location, and various logistical activities inspired the people to up and leave. If a band of militant Arabs in one village was engaged, Arabs in neighboring villages up and left. Here is how Morris describes the rhythm of action:

The UN General Assembly resolution of 29 November 1947, which endorsed the partition of Palestine into two states, triggered haphazard Arab attacks against Jewish traffic. The first roadside am￾bushes occurred near Kfar Syrkin the following day, when two buses were attacked and seven Jewish passengers were shot dead.1 The same day, snipers in Jaffa began firing at passers-by in Tel Aviv. The AHC, which flatly rejected the resolution and any thought of partition, declared a three-day general strike, beginning on 1 December, thus releasing the urban masses for action. On 2 December a mob, unob￾structed by British forces, stormed the (Jewish) new commercial cen￾tre in Jerusalem, looting, burning shops and attacking Jews. Snipers exchanged fire in Haifa and attacks were launched on the neighbour￾hoods of Tel Aviv that adjoined Jaffa and its suburbs. Parts of Palestine were gripped by chaos; the escalation towards full-scale civil war had begun. As in 1936, NCs were set up in the Arab towns to direct the
struggle and life in each locality, and bands of irregulars re-emerged in the hill country. The AHC reasserted itself as the leader of the national struggle.


Strategically speaking, the period December 1947 – March 1948 was marked by Arab initiatives and attacks and Jewish defensiveness, increasingly punctuated by Jewish reprisals. Arab gunmen attacked Jewish cars and trucks, from late December increasingly organised in British- and Haganah-protected convoys, urban neigbourhoods and rural settlements and cultivators. The attackers never pretended to single out combatants; every Jew was a legitimate target. The Haganah also on occasion inadvertently employed terror, as in the attack on Jerusalem’s Semiramis Hotel in January 1948, but normally cleaved to a policy of hitting the guilty and, when not, at least limiting the violence in scope and geographically to areas already marked by Arab-initiated violence.

In January 1948, in line with Arab League resolutions in December 1947 supporting indirect intervention, volunteers (some of them Iraqi and Syrian soldiers and ex-soldiers), mostly under the flag of the newly formed Arab Liberation Army (ALA), began to infiltrate the country. That month, irregulars launched their first large-scale attacks on Jewish set￾tlements with the aim of destruction and conquest – against Kfar Szold in the Galilee, and Kfar Uriah and the Etzion Bloc in the centre of the country.
Some Arabs picked a fight, various Jewish military-like organizations responded. When some  other Arabs saw the response, they begin leaving, with the other factors mixed in. What loomed large in the background was the activities of the neighboring Arab states and the potential for full scale nation-state esque conflict. That eventually happened, leading to the original meaning of "The Nakba" as written by Constantin Zureiq, whom coined the phrase that was later transformed into something else entirely.  Wikipedia describes:

Zurayik is credited with coining the term Nakba (Arabic for "the catastrophe") to refer to the flight of Palestinians in his 1948 book Maʿna an-Nakba.

I have read that book as well. The Nakba in that book is about the loss of the Arab nation-state militaries to the Jewish proto-national military. It was not about "The Palestinian flight" as described in the Wikipedia entry. Here is Zureiq:

Seven Arab states declare war on Zionism in Palestine, stop impotent before it, and then turn on their heels. The representatives of the Arabs deliver fiery speeches in the highest international forums, warning what the Arab states and peoples will do if this or that decision be enacted.
Declarations fall like bombs from the mouths of officials at the meetings of the Arab League, but when action becomes necessary, the fire is still and quiet, the steel and iron are rusted and twisted, quick to bend and disintegrate. The bombs are hollow and empty. They cause no damage and kill no one. Seven states seek the abolition of partition and the subduing of Zionism, but they leave the battle having lost a not inconsiderable portion of the soil of Palestine, even of the part “given” to the Arabs in the partition. They are forced to accept a truce in which there is neither advantage nor gain for them.