If the PCs escape, they might indeed warn the field marshall and get the Korvosan Guard involved. In this case you could have the PCs execute their second raid on the temple with some Guard back-up. Kroft will probably insist on quick action, as she does not want the cultists to abandon their operation - which works in your advantage, for you won't have to make the cultists move base.
As for the Grey Maidens in the Hospice: they are only present in the hospital upstairs. None of them are down in the underground temple and there is no reason for them to know about the Urgathoan operation. They only know that the doctors use the elevator to the cellar, where they have their sleeping quarters. They might not even know about the secret temple and the foul experiments that take place in the underground lair. So, whether or not the Grey Maidens know the truth (that's for you to decide), they have perfect deniability. That is how I played it. In my campaign the heroes decided to keep their involvement in taking out the Urgathoans a secret (wanting to keep a low profile), which gave the Grey Maidens the chance to claim the honour of uncovering the Urgathoan operation and taking it out for themselves. This excused their involvement in protecting the doctors in the eye of the public, since the Grey Maidens were betrayed by the Urgathoan cultists and took care of business as soon as they discovered the truth.
If your PCs manage to escape Urgathoan revenge, but somehow delay their own reaction too long (I'd say, if they don't react the next day), the cultists will kill everyone in the hospitaland flee the city. That would constitue as a failure on the part of the PCs with some dire consequences: all patients in the hospital are dead and the Urgathoans take all documents with them. Since the PCs find no notes on the experiments that the Urgathoans performed, it will take longer to find a cure for the plague and the number of plague victims will be higher. You could even add to the horror by turning the killed patients into zombies who flow out into the city and make even more casualties. Still, I'd have the cultists disappear, as this makes your players feel their failure more than just having them kill the Urgathoans after they have relocated to another hide-out. You could also use key-villains as recurring characters: Doctor Davaulus, Rolth and Lady Andaisin mgiht be back in the future for some sweet revenge ...