|"Hey Ralph, check out this awesome wood paneling."|
The lizard men would do a much better job of being clues to neighborhood unrest if they were found somewhere--indeed, anywhere--other than the boat. Say as a wandering encounter on the way to the Haunted House or in muttered rumours back in town. Preferably both. The problem with having them on the boat is that it would not at all be unreasonable for any normal adventurer to assume that the lizardos are just hired goons of the smugglers and therefore to slaughter them without giving it a thought. But if the Party hears rumors of lizardman encounters in the neighborhood, this, combined with the evidence provided by Oceananus the aqua-elf on the SeaGhost--remember: he tells the Party that he overheard the Cap'n negotiating with some lispy-sounding critters about delivering loads of weapons--raises much more concern that there's a festering lizardman problem than the setup proposed in U1. Maybe take it a step further and have the hold of the Sea Ghost stacked high with Rocket-Propelled-Glaives, concussion darts and some of those awesome shields for which Trampian lizardmen are famous packaged for imminent delivery.
Besides, the presence of the lizardmen on the Seaghost just doesn't make any sense. Few smugglers I've dealt with have ever offered me a hammock in their yacht as part of the negotiations, and I like to think that I make a slightly better house guest than a bunch of fangy, cannibalistic, mud-wallowing lizard fiends. And, as unlikely as it is that a gang of smugglers would offer room and board on their ship, it's even less likely that the lizardos would take them up on the offer; I mean what do they have to gain from sailing around with a bunch of humans unless they're planning on eating them? I can't think of anything, and I'm pretty much the smartest guy you know.*
I think the U-series modules, in order to fit into an old school sand box campaign, needs to be de-railed a bit. So let's say that the PCs roll into Saltmarsh hunting around for an adventure. They hear about the haunted house, but they also maybe catch wind of some lizardman activity in the vicinity. And maybe those lizardmen the folks are skirmishing with are actually Sahuagin, but no one in the village or the party can really discern one species of scaly fucks from the other, not having had a lot of commerce with either species up to now.
Most likely the party will still head off to the haunted house cuz at least they know where that is. And if they survive the Seaghost--big if--then they meet this dipshit water elf who tells them that he overheard the smugglers and lizardmen haggling over a few crates of AKs and a jumbo-sized block of C4. The PCs report this to the Privy Council** back in town and the folks there are all "Run for your lives--there's a Lizardman invasion coming!" So they go into full on panic mode and do what they always do: hire a band of sociopathic outsiders--aka "PCs"--to take care of the problem.
The PCs get to work and track down the lizard lair down at Dunmouth. While they're clearing the place out they find out that the lizards, too, are afraid of an invasion. Perhaps the Sahuagin even attack the Lizardman lair while the PCs are in it; a little Amtraky for a lot of old schoolers perhaps, but something to consider. Anyway, the lizardmen--famous for preferring human flesh to other foodstuffs--are still a potential threat to Saltmarsh, even if they're currently concerned more with the sahuagin, so the PCs don't need a guilt trip over the slaughter they've committed. But maybe they think "Shit, it might be better to help these slimey fuckers out than to kill 'em off" and call a truce. Or not; let the PCs decide.
Essentially, what I'm saying is don't make U2 a Gotcha'. Let the PCs and lizardmen figure out whether or not it's a good idea to drop their hostilities and team up against the Sahuaguin on their own. So forget the were-gild crocodile fiasco; the lizard men can either team up or piss off.
*Good thing you don't actually know me, eh?
**I apologize to my British readers for mangling your municipal governance titles.