First, "manually control" engines and rudder isnt a thing. You're talking about a rudder that could be four stories tall. manual input is physically impossible and you wouldnt want it anyway. screw around with the rudder too much or too quickly and the underway mass of a 500,000 short-ton tanker will rip it out of the ship.
a tanker engine starts at 2.5 stories tall (8-10m). Before ECM and modern SCADA automation these things could take an entire day to start. Everything from fueling to speed and fire suppression are intimately linked through a network on the ship. you can restrict these networks from the rest of the ship but its generally not advised. ship engines communicate with breaker panels, engine controls on the bridge, and telemetry from shipping companies for preventative maintenance.
the solution to this is to have a SOC or rapid response team combined with redundant systems. assume a serious compromise is a failure condition and start the EPO/Mayday.
all it takes is a hacker to add a couple extra zeroes to the idle speed of the engines and youre now a runaway ship, or worse, a runaway engine fire.