(The Talmud is aware of the Hasmonean civil war, by the way; it's mentioned in passing in Bava Kama 82b: כשצרו בית חשמונאי זה על זה היה הורקנוס מבפנים ואריסטובלוס מבחוץ)
As for Pompey, it's in Sforno's commentary to Deuteronomy 28:14:
[Deuteronomy Chapter 28][2] contains a very lengthy, depressing list of horrible things that will happen to the Jewish people if they fail to observe the commandments. Many commentaries suggest that the similar set of verses near the end of Leviticus refer to the destruction of the First Temple, and this track refers to the Second Temple.
Rabbi Ovadiah Sforno (who wrote his commentary in Rome in the early 1500s) observes that there seem to be two discussions of military defeat in Chapter 28; first "a new, sadistic nation will take away your king", and then there are 20-something more verses before "you will be torn out of the land." (Nothing about the oppressor being new at that point.)
He thus writes:
The curses through [28:36], "G-d shall take you and your self-appointed king [to a nation unknown by you or your ancestors]" occurred during the Second Temple, in the times of Antiochus and others, until the Hasmonean kings clashed against one another and one was exiled to Rome by the orders of Pompeyo. The remaining verses, until [28:63], "you will be torn [out of the land]" were until the Temple's destruction by the Romans.