Lo-Fi Games

I was able to kill all 3 main characters in Holy Nation before I even met Flotsam Ninjas and therefore before I talked to Moll.

When I found her relocated to Blister Hill and talked to her first time, she treated me as if we already knew each other and responded as If Phoenix was still alive and she was ready to fight and requested me to talk to her ninjas when ready. But there is no one to talk to and she is no longer "interactable" as well - but the relations with Flotsam Ninjas are at 0.

This seems like a BUG to me, but please let me know if there is something I can do to ally them even though Holy Nation is no more.

Not unless you can bring her one of the three main HN leaders. The dialog for allying is locked if the Phoenix is not okay, and the other dialogs that can ally require bringing her one of the three leaders.

That said, it sounds like there is probably one still up somewhere. As the dialog about talking to her ninjas only happens if one is still alive and free. So theoretically there would still be one at either Stack or Okran's Shield.