Yes, you can take over the battle tower before doing any of the Hall of Echoes quests. Actually you can only do part of that subquest early, in any case, since you need to be able to transform into a dragon to reach the other entrance to the mine.
There is one quest on Sentinel Island that you must do afterwards, as well (getting some treasure from a boat in a tree), though you might want to use the item yourself rather than complete that quest. Any other open quests or areas left unexplored should be done before acquiring the battle tower.
Once you have the battle tower, there is no rush to complete the Hall of Echoes quests. That is the final section of D2:ED, so you should complete everything else before entering (even with the add-on you wouldn't be returning to the fjords or Broken Valley).
