Some scholars have argued that this first comment on Beresheet was, indeed, a reaction to the start of the First Crusade, or at least to its leadup.1
However, in my opinion, the reference to Rabbi Yitzchak makes it clear that at least the original intent of the comment wasn't a reaction to the First Crusade. The identity of this Rabbi Yitzchak is unknown. Many believe that this is a reference to Rashi's father (as suggested for example by the Ta"z in the name of an unknown supercommentary on Rashi), while others think it's a reference to one of Rashi's own rabbis, Rabbi Yitzchak Segan Leviyah or Rabbi Yitzchak b'Rabbi Yehuda (as suggested for example by Rabbi Aharon Asoudry, Chishavti Darki, p. 50 [can be found on Otzar Hachochmah]). A third option is that it's a verbatim quote of a Tannaitic or Amoraic sage from a now-lost midrashic work (for example, Rabbi Yitzchak Miller, Eretz Ha'Galil, p. 456 suggested that this might have been Rabbi Yitzchak Napacha [can be found on Otzar Hachochmah]). Either way, since the Crusade started near the end of Rashi's life, the person who first said this idea was probably long since dead.
Robert Harris, 'Rashi’s Introductions to His Biblical Commentaries', in: Shai le-Sara Japhet: Studies in the Bible, Its Exegesis and Its Language, Jerusalem 2007, p. 293 pointed out another problem with suggesting that this was first written in reaction to the Crusade, which is that by that point in Rashi's life, he had likely taught Beresheet many dozens of times. It's not clear from the text that this was an almost last-minute insertion (although, as he admits himself, there's no textual evidence that clearly proves that it can't be a later insertion).
So, say that it's an earlier comment on Beresheet. What could be the historic background to this? I can suggest that it's connected to a tradition that appears both in Jewish and non-Jewish sources: The claim of the Girgeshites/Canaanites that Yehoshua robbed them of Canaan.
In Yerushalmi Shevi'it 6:1 it says:
"For Rabbi Samuel bar Naḥman said, Joshua sent three orders to the Land of Israel before they entered the Land: Those who want to evacuate should evacuate, those who want to make peace should make peace, those who want to go to war should go to war. The Girgasites evacuated, believed in the Holy One, praised be He, and went to Africa."
And there's also the story in Sanhedrin 91a of the African Canaanites coming to Alexander and demanding he take Eretz Yisrael from the Jews and give it back to them.
While the 6th-century historian Procopius wrote (The History of the Wars of Justinian, IV):
"In that country there dwelt very populous tribes, the Gergesites and the Jebusites and some others with other names by which they are called in the history of the Hebrews. Now when these nations saw that the invading general was an irresistible prodigy, they emigrated from their ancestral homes and made their way to Egypt, which adjoined their country. And finding there no place sufficient for them to dwell in, since there has been a great population in Aegypt from ancient times, they proceeded to Libya. And they established numerous cities and took possession of the whole of Libya as far as the Pillars of Heracles, and there they have lived even up to my time, using the Phoenician tongue. They also built a fortress in Numidia, where now is the city called Tigisis. In that place are two columns made of white stone near by the great spring, having Phoenician letters cut in them which say in the Phoenician tongue: "We are they who fled from before the face of Joshua, the robber, the son of Nun.""
It should be noted that this tradition is also mentioned (col. 1047, highlighted) in the Latin translation of the Chronicon Paschale, and the now-lost original Greek core of this text, which is dated to the 3rd century BCE, likely also had this tradition, which makes this tradition even older.2
Rabbi Yitzchak's statement makes sense in such a context: Like Rabbi Shmuel bar Nachman who properly contextualizes the Girgeshites' immigration to Africa (based on a belief in Hashem) and like Geviha ben Pesisa's argument in the Alexander story, Rabbi Yitzchak produced a response to potential Canaanite descendants (or really anyone) who wished to claim right over the land.
1 See for example: Elazar Touitou, 'Rashi's Commentary on Genesis 1—6 in the Context of Judeo-Christian Controversy' (different link), HUCA 61 (1990), p. 171; Ivan G. Marcus, 'Rashi’s Historiosophy in the Introductions to his Bible Commentaries', Revue des Études Juives 157 (1998), pp. 52-53; Harvey Sicherman and Gilad J. Gevaryahu, 'Rashi and the First Crusade: Commentary, Liturgy, Legend', Judaism 48 (1999), p. 2 (in the PDF link).
2 For more information on non-Jewish sources that reference this tradition, see Anthony J. Frendo, 'Two Long-lost Phoenician Inscriptions and The Emergence of Ancient Israel', Palestine Exploration Quarterly 134 (2002), pp. 37–43; idem, 'Back to the Bare Essentials, “Procopius” Phoenician Inscriptions: Never Lost, Not Found’ — a Response', Palestine Exploration Quarterly 139 (2007), pp. 105–107.