Your reviewers are correct that "don't" is informal. Whether it's appropriate to academic writing or not is a harder question to answer. Google Scholar turns up 2 million hits for "doesn't" and 2,800,000 for "can't," so clearly it's used in some academic contexts. (The results for "don't" weren't helpful, since Google flagged not just "don't" but the name "Don T.")
Whether it's appropriate for your specific journal or conference depends on their overall style. I would pay attention to the other papers presented there to see how formal they are, as well as trying to find out what specific style guide the journal uses (maybe by asking their editor or checking the journal's website--frequently guidelines for writers are listed somewhere on a journal's page).
Another thing that might help identify whether it's a common convention is how many reviewers pointed it out. If one reviewer noted it, and three others didn't, it may well be one person's preference. But if multiple reviewers found it problematic, that suggests that it will seem out of place to the journal's audience as well.