There'd be limits to that, too. The effects of the gas would only last so long, requiring a second dose and a third and a fourth one before everything necessary could be achieved. Somebody would eventually die. All the more so because our two heroes could not know how long this "so long" would be for each of the exotic lifeforms currently on board... And whether they could be stunned at all.
Yes, and don't forget they've got children on board too, who would definately need a lower dose than adults.
The problem with gas is that today, certain forms can be used as an anesthesia. But these are carefully regulated by doctors on an individual basis, since there is no such thing as a universal dose that affects everyone the same way.
Enterprise (the show, not the TNG ship) gassed the whole ship in their Ferengi episode, (which wasn't even a very good episode anyhow). But at least Enterprise had mostly human adults. I don't think Genesis in TNG would have been a better episode for using this trick.