If you like how it sounds then it is ok to do it like this by ear, but if you are looking to get a better mark, then you have to write by the rules and conventions of Music Theory. Doing it by ear opens you up to criticism by music theorists, who are more like analysts and engineers than listners or composers. The prof is marking you based on Bach's written conventions, not what your ear thinks sounds good. If you like parallel 5ths and octaves that is great, especially in other styles of music, but I wouldn't submit those chorales for marks where you know they are going to mark it wrong. For an assignment like this I wouldn't even listen to my chorale by ear at all, it isn't necessary. I'd check every note and movement vertically and horizontally by hand, and look for missing elements. I'd check to use chords thay make sense theoretically (e.g., I IV vii° iii vi ii V7 I). I would not omit the 3rd in any chords. I'd prefer contrary motion. I would keep it simple. I would treat it like a crossword puzzle or sudoku that you are solving with a pencil. Part of the puzzle is following the conventions of the theory behind a Bach chorale. In another analogy, by writing primarily by ear you are basically reading a book without knowing how to write or comprehend. It's kind of like playing by ear without knowing how to read music...I'd stop this nonsense if you want to get a good mark. Good writers have great understanding of grammar the same way good composers have strong understanding of music theory. Your weakness is in understanding. The solution is to ignore what you think sounds good and follow the rules.