I don't believe this will cause any problems for you. She has no role beyond this chapter. FYI, I saved her. After this, she offered me some healing and wanted to charge me for it, AFTER I HAD SAVED HER LIFE!!! I almost killed her right there for the ingratitude.

Location: Dragon's Eye, I believe it's about the 3rd level, the Talonite priests' lair...
OK, here's what happened: while fighting with those goddamn priests, my mage launched
a fireball towards them and hurt Mother Egenia, who was initially neutral (bluish circle
around her). After I was done with the priests and trolls, I go to Mother Egenia, she's
hostile now (red circle). I heal her thinking she appreciate that. No, she still won't
talk to me. Frustrated, I whip out my big-ass sword and beat the hell out of her...

Now my question is: did I screw up some quest by killing her? Who was she?
Any help appreciated...

Ah, you didn't really lose much; however, she's a priest and she heals and raises dead. So I don't think killing her is a good idea. She's also the only place in Dragon's Eye that you can safely rest without a chance of having a monster appear. I would keep her alive if I were you. She also gives you some experience points. Don't know how much since I finished the first game without the patch. Hope that helps!

Try casting charm person on her, then chatting using the talking heads symbol on the main screen. You have to do that each time you come back as she's annoyed that you burned her best wig...

Erm... just for the record:
you can also rest with Marchon after you've freed him and his people and the summoner's dead in the main room.