I have also been bothered by this exact question and I have not found an answer inside. The Maharal does deal with this midrash in Beer HaGolah 6:2, but his focus is more on explaining how eclipses indicate sin, especially given that they are predictable astronomical phenomena. My initial thoughts are (1) as @Harel13 says above, I'm not particularly troubled by the Islamic calendar because it post-dates the Talmud. It may also be partly based on the Jewish calendar. See https://en.wikipedia.org/wiki/Islamic_calendar. (2) Even though there are pre-Talmudic cultures that used the lunar calendar, 
https://en.wikipedia.org/wiki/Lunar_calendar, we could say the Talmud is speaking in generalities and doesn't mean every non-Jewish culture uses a solar calendar.

But two additional problems are (A) the Jewish calendar is based on the moon *and the sun*. So why don't solar simanim also affect the Jews? This svara would support the first Baraita that a solar eclipse is bad for the whole world. And (B) the Babylonians used a calendar very similar to the Jews, including the same lunar months and a 19-year Metonic cycle of intercalated months. So which "goyim" exactly are they talking about? Perhaps when they say "goyim" they really mean Greece and Rome (which is probably what the Tanaim who authored those Baraitot would have been most interested in). You could probably come up with some nice chiddushim there about the sun and the moon and Jacob and Esau.