A lot of pilots don't use ILS and use a visual approach. That was one of the issues with the SF airport, as the left runway was closed, the lights were off and the pilot lined up with the taxi way.
While it is true that the normal lighting was off (because it wasn't a valid runway at the time), there was a lighted, flashing X to indicate that fact. Along with the fact that the taxiway was not illuminated as a runway, and the pilots were notified about the runway closure…
This is being downvoted, though is true to my understanding -- not uncommon for even the largest airports to have both ILS and non-ILS runways. (e.g. Runway 1L at SFO is non-ILS.)
In this particular case, the departure airport only had one runway, and immediately after the botched takeoff it was at least in dire need of a debris check, so I wouldn't be surprised if the airport was closed while that happened. Wouldn't have taken four hours, though, and I suspect that they would do whatever they could to accomodate an emergency aircraft had the pilot declared.