I no longer remember that playthough, but I had the same weird dialogue about Marcus "being upstairs with Isobel" while I had killed him already ...
You can get to Moonrise before Last Light Inn if you accompany your Friendly Local Drider Guide and beat off the ambush by ... bandits :P
BTW - I wonder if it is possible to get to Moonrise Towers without either pixie lantern or Selune's blessing - by way of the pier?