Why is being an inherently unfriendly adult drow a reason for getting slaughtered, when being an inherently unfriendly big fish with a crossbow isn't?
Also, you're not exterminating an entire race. You're destroying a single colony, which happens to be close to both a Svirfneblin settlement and the surface, and thus able to pose a threat to lots of generally Good people.
Well, you can either kill the Egg Guards before opening the door, or open the door before killing the Egg Guards. If you take the first path, you only have to kill 2 Drow. If you take the second path, you have to kill every single Drow that sees you on your way out of the city. Now, you can't exactly
know this all beforehand, but it's pretty obvious that if the Guards
see you just waltz into the top-security vault they're guarding, they'll raise the alarm.
This situation could use a tweak, though: The only reasons the Guards
wouldn't start yelling is if they were convinced of your permission to enter the Vault (in which case, the Golems should leave you alone, too), or if you killed them both
at the same time. A Solo player would find it nearly impossible to kill both of them in the same round, so I suggest that either one of the Egg Guards should be removed, or a small conversation be written so that a player with the Despana Treasury Key can exert his authority to enter the vault unhindered.
As for the Kou-Toa....I think the Virtue drop being associated with the Tadpoles reflects on the idea that the young of a species (any species) are inherently Neutral, and even Evil races can be trained Good if raised in the proper environment, so infecting the young for the sake of their parents' sins can be called unvirtuous. There's also the fact that the Kou-Toa are total pansies, and there's no need whatsoever to contaminate their young in order to weaken the population as a whole (well, a Solo player might need to do it in order to kill the Prince, but that's pretty much it). If the Svirfneblin can survive right next to a Drow city, I'm sure they have no trouble with the Kou-Toa.