Take a look at the original sentence again:
Susan ducked down when she saw Mr. Hayden, her English teacher, walk into
Tito's Taco Palace, unfortunately, a burrito
wasn't big enough to hide behind, so poor Susan had to explain why she had
missed his class again.
You chose to fix it the correct way:
Susan ducked down when she saw Mr. Hayden, her English teacher, walk into
Tito's Taco Palace. Unfortunately, a burrito
wasn't big enough to hide behind, so poor Susan had to explain why she had
missed his class again.
Susan ducked down ... begins a complete sentence. Unfortunately, a burrito wasn't big enough ... starts the next sentence. You are always correct when you use a period and a capital letter between the two sentences that create a comma splice.