I'm not a teacher, just a US native speaker. I feel sure that the correct grammatical answer is that the subject of the sentence is "flock." "Of geese" is just a phrase that modifies the word flock. It tells you what kind of flock it was. Therefore, the subject is singular and the correct pronoun is "its." (By the way, congratulations on spelling "its" correctly, without an apostrophe.) Some sentences with similar structure would be:
The army has its headquarters in Washington.
The orchestra was following its conductor.
The circus was going to its winter home in Sarasota.
The flock was following its leader.
The big flock was following its leader.
The flock of geese was following its leader.
We could also make "geese" the subject. In that case it would be plural and the right pronoun would be "their."
The geese were making their annual migration.
It was summer and the geese were losing their feathers.
The geese were following their leader.
The geese were in a flock, following their leader.
In real life, native speakers often make mistakes with sentences like this. When it comes time to say the pronoun, we are influenced by having said the word "geese." We are quite likely to make a mistake and use the plural pronoun. This kind of mistake happens quite often and usually goes unnoticed. However, speakers "feel" the structure of the sentence in their mind, and remember that the subject is "flock" even though they have spoken the word "geese" afterwards.