Yea GilesIgnoreStuff is your way to go. In his code he made a bool that can be set easily so the bot wont use shrines at all
open the .cs and look for the following line:
private static bool bIgnoreAllShrines = false;
Set it to true and it should ignore all shrines
The chest might be a little harder since its distant dependent. But if you study it closer I think you can set the distance to something so close that the bot wont open anything. Might be some much easier way tho to do this...