Could a journal reject an article due to the style or quality of accompanying code?
You will not have a paper rejected for poor coding style. Particularly not in bioinformatics. Unless the paper is a tool development paper, the chance that a reviewer even looks at the code is not that high, and if they do, it will just be to check that its reasonable. In the outside case a reviewer might spot a bug, or poor assumption that actaully makes the result wrong, but they will not reject you for poor style.
However, having the code associated with the paper massively increases the chances that it will be useful to someone else.