I do get annoyed when semi-literate editorial assistants insist on changing "don't" to "do not" and thereby change the rhythm of a sentence. Don't write what doesn't sound good to the ear; if the natural shape of a sentence seems to call for a contraction, then use it. And I say this as someone who edited a journal for twelve years, and having just sent another book off to press with oodles of contractions.
If you find writing with zest and lively naturalness means using occasional contractions, do so (within reason). If a stodgy editor tells you to remove the "don't"s and "won't"s later, then you might have to sigh and conform. But the more people send in articles in a lively readable style the better, and the more chance of journals relaxing their sometimes over-conservative style guides.