One normal "trick" is phantom typing. You create a type representing indices and have a small, well-audited portion of unsafe code handling creation/unpacking, where the rest of the code is completely safe.
The details depend a lot on what you're doing and how you're doing it. Does the graph grow? Shrink? Do you have more than one? Do you care about programmer error types other than panic/UB?
Suppose, e.g., that your graph doesn't change sizes, you only have one, and you only care about panics/UB. Then you can get away with:
1. A dedicated index type, unique to that graph (shadow / strong-typedef / wrap / whatever), corresponding to whichever index type you're natively using to index nodes.
2. Some mechanism for generating such indices. E.g., during graph population phase you have a method which returns the next custom index or None if none exist. You generated the IR with those custom indexes, so you know (assuming that one critical function is correct) that they're able to appropriately index anywhere in your graph.
3. You have some unsafe code somewhere which blindly trusts those indices when you start actually indexing into your array(s) of node information. However, since the very existence of such an index is proof that you're allowed to access the data, that access is safe.
Techniques vary from language to language and depending on your exact goals. GhostCell [0] in Rust is one way of relegating literally all of the unsafe code to a well-vetted library, and it uses tagged types (via lifetimes), so you can also do away with the "only one graph" limitation. It's been awhile since I've looked at it, but resizes might also be safe pretty trivially (or might not be).
The general principle though is to structure your problem in such a way that a very small amount of code (so that you can more easily prove it correct) can provide promises that are enforceable purely via the type system (so that if the critical code is correct then so is everything else).
That's trivial by itself (e.g., just rely on option-returning .get operators), so the rest of the trick is to find a cheap place in your code which can provide stronger guarantees. For many problems, initialization is the perfect place (e.g., you can bounds-check on init and then not worry about it again) (e.g., if even bounds-checking on initialization is too slow then you can still use the opportunity at initialization to write out a proof of why some invariant holds and then blindly/unsafely assert it to be true, but you then immediately pack that hard-won information into a dedicated type so that the only place you ever have to think about it is on initialization).
[0] https://plv.mpi-sws.org/rustbelt/ghostcell/