It seems like both... don't sail into a hurricane and there's no problem, right? But even their sailing into it was an interaction of many factors -- the captain's insistence, predicated on preferring the graphically vivid but outdated weather maps, and on disregarding the opinions of his officers, and on each of them independently failing to be sufficiently assertive (or even convinced of the danger themselves) to change his mind.
There's also the broken anemometer, but I'm tempted to discount that, because it was obvious the wind was from port, indicating (in any counter-clockwise-rotating storm, i.e. any cyclone in the northern hemisphere) you are headed right into it. Winds should have been from astern if you were trying to cross in front of it. When you're convinced of something, sometimes you can stare right at contrary evidence and disregard it. But who knows, maybe having an accurate wind reading would've jogged some brain cells.
If the engine was kept running as you say, that might have helped them, but only if they had used it to turn and get the hell out of there. If the captain insists on using it to continue driving straight into a hurricane, it just makes things worse. And then of course there's all the water they took on, limiting their getaway speed so to speak. In a certain way it seems like the point of no return was the rupture of the fire water inlet. No telling what the ship could've withstood if they had secured the load better and secured the hatches better. Unfortunately all you get with this kind of hindsight is all the things that went wrong, not necessarily what would've had to go right.