The Edinburgh Trader massacre is arguably much sadder if you think about it from Will's POV.
Because Will was the sole survivor. The movies don't pay what I'm about to say very much mind, so I'm admittedly probably overthinking things a little, but please just hear me out.
It obviously sucks that a ship full of innocent men got torn apart and killed, but you know what else is unfortunate? It's heavily implied that Will blames himself for the whole thing.
Just moments before the Kraken attacks the ship, Will says "I've doomed us all" because, remember, he was the monster's main target for stealing Davy Jones's key. Also, Will's face when the Kraken splits the ship in two says more than 100 words in my opinion. He only knew those men for a few hours at most, but long enough to know that they didn't deserve their deaths at all, seeing as how they were at least kind enough to pick Will up in his longboat and let him rest. And yet people wonder why Will was so dead set on killing Jones on Isla Cruces (well, apart from that it would free his father).
But the unfortunateness doesn't even end there!
So the trilogy ends with Will killing and replacing Jones, meaning Will has to ferry souls in the Locker to the next world, right? Naturally (albeit offscreen), amongst those souls would be the Trader's crew. They'd recognize Will's face and, since they knew he was running from the Flying Dutchman before the Kraken showed up, I personally wouldn't put it 100% out of the question for Captain Bellamy and his men to shout things like "YOU KILLED US" at Will. And he wouldn't even argue otherwise if they did, for the above reasons I've already stated; he'd still ferry their souls just as he would anyone else's. Either way, Will had to confront his own guilt offscreen, knowing he'd turn into a sea monster like Jones if he didn't. At least he'd still have his (equally guilt-ridden) father to talk to in that case...
TL;DR: The Edinburgh Trader massacre is one of the most underratedly tragic scenes in the whole trilogy, and Will's trauma from the event shouldn't be overlooked in my opinion.