Q:

石が足を取られて grammar

その石が足を取られて転ぶほど大きいのか、それとも裸足で踏んでも気にならないほど小さいのか

Was the rock big enough to trip me up, or was it so small that i didn't notice it despite being barefoot.
I don't have the context for this sentence, it was the example sentence i have for 足を取られる.
Nonetheless, the use of その石が with the passive verb is confusing, compared with something like 水に足を取られて派手に滑って転ぶゾウの貴重なムービー
why is it not その石に足を取られて?

A:

The basic structure of this phrase is:

その石が大きいのか、それとも小さいのか
  whether the stone is big or small

That is, その石 is not the subject of 取られる but the subject of 大きい and 小さい. 足を取られて転ぶほど is an modifier that adverbially modifies 大きい, and it has a different implied subject (誰か "someone" or 私 "I"). Read it like this:

その石が([誰かが]足を取られて転ぶほど→)大きいのか、それとも([誰かが]裸足で踏んでも気にならないほど→)小さいのか

Actually, your translation attempt already reflects this structure correctly.
(Technically, 石が足を取られる in isolation can form a valid indirect passive structure, but it makes no sense because a stone does not have legs.)

