Before writing the article about religious minorities, try to learn more about the group and to spend at least one day with the representatives of this community by studying their practices, watching how they contact with people. There is no need to take side with their religion, but this experience will let you know these people better.
Try to figure out what has caused stereotypes about a given religious community and why? Which external factors in your country (law, freedom of expression and belief, level of critical thinking of the audience) have impact on the perception of a given religious minority? Ask experts and scholars about it.
Do not set the religious minority against the society: there are possibly people in the community who are good specialists and contribute to the national development.
Do not focus on the immediate event or a conflict that takes place with participation of the religious minority and its consequences. Look into the roots of the problem that often have nothing to do with their religious affiliation.
Put facts into your context, and describe a possible solution to a problem in analytical materials and journalistic investigations (if relevant), via interviews with experts. However, do not incite debates about this decision in your report until your audience is prepared to accept the religious diversity.