The phrase "cruel way" refers to a harsh or unkind manner of doing something. It means that someone is being mean or causing pain to someone else. Full definition
Pregnancy can be really cruel that way: Your body demanding food but actively rejecting the food you offer it. (barebonesbroth.com)
Might not the first two be accomplished in more effective, more moral, less cruel ways? (firstthings.com)
... In a contrary and perhaps rather cruel way the twentieth century has relieved us of labor without at the same time relieving us of the conviction that only labor is meaningful. (religion-online.org)