This is where the power of scripting comes in.
For example (need to first uncomment the line in the config):
#!/bin/bash
CONTAINER_NAME=storagenode
CONFIG_PATH=/mnt/storj/config.yaml
docker container stop $CONTAINER_NAME
sed -i "s/^storage2.piece-scan-on-startup: .*/storage2.piece-scan-on-startup: true/g" $CONFIG_PATH
docker container start $CONTAINER_NAME
sed -i "s/^storage2.piece-scan-on-startup: .*/storage2.piece-scan-on-startup: false/g" $CONFIG_PATH
However I do agree with having more feature rich APIs. It would be nice to start/stop filewalkers and query their status from the web API.