I found this by chance. A piece by Amram Tropper adressing the story of Raban Yochana Ben Zakai download the pdf link at http://www.torahmusings.com/2005/08/rabban-yohanan-ben-zakkai/
His theory concerning the question here is that Chazzal were trying to present Rabi Yochanan Ben Zakai as a Jeremiah like figure. This main point begins on pg 140, pg 8 of the pdf.
The questions he was addressing were why Chazzal chose to present Rabi Yochanan Ben Zakai in what he thinks is an unflattering light, possibly even dangerous considering the authorities.
What I take out of it is the imaginative way he takes the portrayal of the story of Raban Yochanan Ben Zakkai. At the same time he applies this same imaginative portrayal to Josephus about himself.
Here's some excerpts.
In broad strokes, the comparison between Jeremiah’s activities at
the time of the destruction of the First Temple as reported in the Book of Jeremiah, and Rabban Yohanan ben Zakkai’s actions as described in the literary kernel of our legend, can be articulated as follows. A Jewish leader living in besieged Jerusalem opposes the war, foresees the city’s destruction and therefore calls upon the Jews to surrender. His appeals, however, remain unheeded and the city’s situation deteriorates. When he realizes that the destruction of the city is looming, he seeks to flee the city but runs into difficulties with the Jewish guards at the city gates who oppose his exiting the city. In the
long run, his anti-war stance serves him well and when he comes to the attention of the enemy leader, he is rewarded for his support. This sketch of a leader’s actions at the end of the Temple period is quite remarkable because it applies in equal measure to both Jeremiah and Rabban Yohanan ben Zakkai.
The notion that the rabbis would have portrayed Rabban Yohanan
ben Zakkai as a second Jeremiah presupposes that they interpreted the destruction of the Second Temple in light of the destruction of the First and indeed, scholars have noted that the rabbis did interpret in this manner.
This interpretative approach is perhaps most apparent in the manner that Lamentations Rabbah interprets Lamentations, a book composed in reference to the destruction of the First Temple, to refer to the destruction of the Second Temple, as well.
Moreover, the rabbis were not the only Jews to project a Jeremiah-like figure into the Second Temple context; Josephus also did so. By stressing his own prophetic capabilities, his exhortations to the Jews to surrender, and the subsequent assaults on his person, Josephus portrayed himself as Jeremiah reborn.
Returning to our question, how the rabbis could risk portraying
Rabban Yohanan ben Zakkai as a deserter and perhaps even as a
traitor, as “a friend of Caesar,” it appears that the answer lies with Jeremiah.
Although it is likely that the story of Rabban Yohanan ben Zakkai’s escape was influenced, at least in part, by some version of Josephus’ escape, the rabbis’ willingness to incorporate such a problematic account into their own foundation legend should not be explained as a careless incorporation of foreign materials.
Rather, the emotional distance and accommodating stance to Rome of amoraic times made it possible to tell Rabban Yohanan ben Zakkai’s escape story, while the paradigmatic understanding of the destruction of the Temple in conjunction with Jeremiah’s account of the first destruction, made it desirable.
Despite the many differences between the careers and historical contexts of Jeremiah the prophet and Rabban Yohanan ben Zakkai the sage, Jeremiah’s narrative heavily influenced the portrayal of Rabban Yohanan ben Zakkai’s journey from Jerusalem to Yavneh.
Perhaps this escape story, when all is said and done, risks appearing unflattering, but, for the rabbis, it was the type of story one told about the destruction of the Temple.