I suppose that I start with a noble purpose (no Pickpocketing, no Shoplifting, all Friendly NPCs near me have to survive the battle). But then I realize that, both the party and the Dark Savant have both good and evil in them, as alluded to by Marten's Ghost.
In theory, you could murder anybody, with instant death magic (Instant Death, Asphyxiation, Death Wish, Quicksand), and there would be no reaction from any faction. I wonder if this is an exploit, or if this was done on purpose.
This is certainly a concern with the Rapax. For example, you could plow through the Rapax Rift, Courtyard, and Rapax Castle Main Level, and do a certain thing for Al-Sedexus that we won't talk about here. From now on, your faction rating with both the Rapax Common and Rapax Templar are set to Friendly. After slaying your lover, you are now free to leave the Rapax areas (provided you Webbed/Paralyzed/KOed her before she could summon reinforcements).
Now you are official Rapax Templar, and you can visit the Rapax Away Camp without any problems. The Rapax King has his wife, the Rapax Queen, locked away in her cage, and he instructs you to interrogate the Umpani and T'Rang prisoners. Of course, after talking to Drazic and Rodan, you can portal them away to their leaders, but this ruins your faction rating with the Rapax.
Or, you could force your way into the Rapax Away Camp, after having gotten at least 2 artifacts, before visiting the Rapax Castle. Your faction rating with the Rapax Templar starts at Neutral, and you get a friendly warning. However, just push your way in. All Rapax in the immediate area declare war on you, but if you were smart, and high enough level, you would use instant death magic against them. Your faction rating with the Rapax Templar should still be Neutral. Once that battle is over (and a few more minor, unimportant battles remain), you should have cleared most of the Rapax Away Camp, including the Stockade Guard (getting the key to rescue Rodan and Drazic).
Of course, talk to the bratty Rapax Prince, while he teleports away (and his Concubines attack you). This leaves just the Rapax King and his assistant, who isn't special in any way. Kill the assistant with normal instant death magic.
The Rapax King is immune to instant death magic, so must be killed in the normal way, as you would handle any boss (melee combat). However, this will reduce your faction rating with the Rapax Templar, going from Neutral to Hostile. This is why you handle the Rapax King last.
So now your faction rating with both the Rapax Common and Templar are both Hostile. No love lost, as that's just the way it is. Plow through the Rapax Rift, Courtyard, and Castle Main Level, and do the Al-Sedexus quest. Now, your faction ratings with both the Rapax Common and Rapax Templar are permanently set to Friendly, and you can visit Ferro in peace.