A couple of points have emerged to help clarify things.
So, I can put this together. Only one thing will make an engine produce that enormous quantity of black smoke and that is a hole in the top of one of the pistons.
So then engine shut down as it should with this catastrophic failure, but because of their situation the crew over rode the shut down. The power came back briefly, but the damaged piston shattered and locked then engine up, and made the catastrophe inevitable.
Ships should NEVER get their power from the same engine that powers the propeller. That alone would likely have prevented this.
The ship had two diesel engines. A large one generated electric power to drive the single propeller as well as providing electric power for steering and other needs on the ship. A second smaller auxiliary diesel engine was available to provide electric power for steering and other uses if the main engine/generator failed.
The Mayday call came by radio after the ship lost power. Was that done by a battery powered hand-held radio, or had the auxiliary diesel electric come online?
It is possible that the two emissions of smoke could be explained 1) by failure of main engine, and 2) by the auxiliary engine as it started. The investigation will probably clear that up.
First the bridge should never have been designed like that to allow for that type of catastrophic failure. The bridge was built in 1977, and that design would not be allowed now. So that bridge should have already been replaced on that account.
Next the bridge should allow for ships and their tugs to stay attached until past the last bridge to the sea. The tugs had just left that ship before it went into the bridge.
The collapsed bridge was a continuous truss design that was in use when the Key Bridge was designed in the late 1960s. When built with a 1,200 foot span, it was the third longest continuous truss bridge in the world. It had 4 traffic lanes, and was strong enough for anticipated use when designed, as well as recently.
That continuous truss design is no longer built anywhere. It seems cable-stayed bridges of similar length are now commonly used instead. I'm not sure why, but it's probably cost. It is said that cable-stayed bridges are optimal for spans longer than steel truss/cantilever bridges, but shorter than suspension bridges. They have replaced older steel truss/cantilever bridges, and are favored for new construction in that span range. For longer spans, the previously used steel truss/cantilever bridges become too heavy and more costly, while the cabling for suspension bridges would be more costly.
Cargo vessels in the late 60s and early 70s were about one third the size and weight of those presently used. A 1,200 foot span was adequate by the design standards of the time.
Just why the two main support pylons were placed 1,200 feet apart is not clear. The shipping channel depth was about 50 feet, and about 30 feet at the support pylons. Perhaps the shallow water at the river's edges was enough to prevent large ships from entering.
Obviously, a new bridge will have a longer span, as well as providing more than 4 lanes for traffic. The support pylons will have to be at the river's shore or close enough to the shore to prevent large ships from hitting them. It will probably be a cable-stayed design.
I don't think protective cut-waters can be built large enough to protect the support pylons from 100,000 ton ships. It may be possible, but only at a prohibitive cost.
A more expensive alternative would be a tunnel. At the time the Key Bridge was built, it was the only way trucks carrying hazardous materials, such as gasoline, could cross the Patapsco River. Two tunnels exist further up river, closer to Baltimore, but hazardous cargoes are prohibited in them. For that reason only a bridge was chosen.