You did one thing right, you did not blindly follow your teachers instructions without thinking about them first.
It is true that certain fingerings are needed to produce a certain type of tone, but when the teacher insists on fingerings in the manner that your's has I highly quesiton her teaching. Fingering is independent to physilology, and the shape of your hand and body. You have to use a fingering that is most natural to your hand, and helps you to control the passage to the best of your ability.
The fingerings printed in books are only suggestions, and if any particular one doesn't fit it is wise to change it to one that does.
It seems as your teacher relying to heavily on fingering to produce a certain sound. There are many other elements that go into producing a particular tone, and you should be able to prodce that sound with whatever fingering works for you.
Following fingerings in the books has the advantage of teaching you a new fingering for a specific pattern. So yes it is good to try those suggested fingerings, as you may learn something from them (maybe even better than what fingering you would have used). But after trying after a few days, if you still don't feel comfortable, you should consider changing the fingering.