We fully intend to finish Conqueror's story arc once conqueror is updated to the new SS2 standards (it should run better as well). As the primary writer for conqueror, I can tell you that writing has definitely resumed for it. Like Uituit said... to get the full conqueror experience from start to finish (the whole story), you'll need to wait for the SS2 version, as the story will not continue in the old SS1 format.
Having said that, if you want to get to the end of the current story content, you still have a ways to go, as there are still several quests (and a few plot developments) after the Burden to Bear quest (which from your description seems to be where you left off).
Having said all that, I will also say you may see a few familiar faces from conqueror turning up in SS2 as well, and it's worth your time to explore its story.