I ended up using a slightly modified version of VDR’s solution which waits for the sqlservr to start by checking the logs instead of sleeping 10 seconds:
RUN ( /opt/mssql/bin/sqlservr --accept-eula & ) | grep -q "Service Broker manager has started" \
&& /opt/mssql-tools/bin/sqlcmd -S localhost -U SA -P 'P@ssw0rd' -i /opt/mssql-scripts/000_create_db.sql \
&& pkill sqlservr