I think the simple answer is that it is not easy. To start, rigorous design processes with risk analysis upfront are certainly necessary, as are well-defined operational contexts for the autonomous functionality, and a very disciplined approach to clearly defining safety-critical subsystems and minimizing their surface area.
There's a surprising amount of work in the literature that serves as a guide for using neural networks in safety-critical contexts, e.g., http://dl.acm.org/citation.cfm?id=2156661 and http://dl.acm.org/citation.cfm?id=582141.