The citizens of San Clemente have been able to figure out how to coexist with at-grade-pedestrian rail crossings. Here is world traveler Justin in front of at-grade crossing number 1.
Crossing number two gets tons of pedestrian traffic. It allows hundreds of people a day to get to the beach and pier. The crossing isn't much. The red circle shows the crossing.
Here is a link to a S.C. Pier/train crossing webcam. You can watch people cross safely.
Crossing number 3.
Yes, people have been hit by trains in S.C. People walking/riding on the tracks have been plowed. Many of them were near Trestles and they were doing dumb crap like wearing headphones or trying to race the train. Pedestrian tunnels would not help these people, especially at Trestles, where you can already opt to cross under the trestles to get to the beach.
See Also: Inconceivable and Encinitas At-Grade-Crossings.