It's obvious that whatever now exactly happened when things went pear-shaped, it was a wake-up call that caused the known project staff members take a good long look at what they were doing and not like what they saw at all. Saria and Silence definitely have nagging consciences over the whole thing (though the latter's seems more Ifrit-specific as many of her lines still carry a certain mad-scientist undertone). Ptilopsis might too but it's hard to tell given she's currently busy pretending to be a damn computer to hang on to what's left of her sanity; "-- a necessary measure to prevent the system nexus from being devoured by that other voice." Creepy, esp. if it's somehow connected to the "enormous apparitions" in Iffy's hallucinations...
Incidentally the fact that Rhine was apparently willing to let Silence just walk away with the valuable if volatile research subject (instead of doing the usual villainous megacorp routine) implies the company probably considers the project finished and that line of inquiry exhausted. The ex-staffers are presumably nevertheless under some heavy NDAs, which are probably further reinforced by the implicit threat of hit squads if they're found to have blabbered about sensitive details...