Masonic funerals are only an adjunct to actual religious services and do not substitute for them in any way. The main idea is to help console the bereaved, letting them know that a group of men they might not have even been very aware of is now dedicated to ensuring that they are helped whenever possible.
In the ceremony, an apron will be draped over the coffin (or some appropriate item relative to the deceased, if cremated) and sprigs of acacia will be strewn. That’s all. The fear does sound unfounded and you should feel confident in reassuring your sister on the point.
When my uncle died, a man who had been a dedicated Mason, his whole life, my aunt arranged a funeral to accommodate a large number of Masons. She was disappointed that they never showed up. Of course, he had retired and was buried from his home town, not where he had lived the last twenty or thirty years.