I don't think you necessarily have to keep them from 'finding out' but either way, you still have some potential tools to complicate matters:
- Your NPCs can object. Heck, maybe someone like Clayton even starts trying to manipulate them with promises of money and such. Your PCs may start getting a bit murderhobo-y and threaten to kill them if they don't, so...
- One or more of the NPCs can attempt to escape from the PCs (and everyone else) before they get scanned. Maybe they're just too afraid with the PCs pointing guns at them.
- The module suggests the whole crew is infected, but maybe have one (maybe the first scanned) have had their serum work properly for them (it has a chance to work for the PCs after all if they're infected). Having one pass may help buy time for manipulation/uncertainty/etc.
- Maybe the PCs even get so far as to scan one person and find they're infected, and chaos fueled by fear erupts from the rest. And if the PCs DO make good on their threat to kill them, make them roll for coup de grace, since the NPCs are very much helpless.
- Have one of the abominations/neomorph interrupt the attempt by the PCs to do so. Have the NPCs scatter when that happens.