Indeed - we design systems to operate under the expectation that services are available. We handle their not being available as an exceptional case.
This seems analogous; we should design social structures (or allow social structures to emerge) that assume that individuals are male or female, but which handle the exceptional case of non-cisgendered individuals. Just like a software system that doesn't handle exceptions gracefully, a social system that lacks provisions for these is fundamentally flawed and can fail unexpectedly and potentially catastrophically.
Society also lacks "provisions" for violent criminals[0] but it still handles them and is yet to fail catastrophically.
[0] I'm not equating these two categories of people, merely illustrating that your example of comparing software exceptions to people is deeply flawed.