I don't know how you can change the rotation handle's rotation without effecting the geometry. However, I do know how to change the objects rotation without effecting the rotation handle. Perhaps this will get you in the right direction.

Select the object and open up it's attributes. Go to the transform attributes and then change the rotation axis as needed. See attached image. So, if you wanted to, you could set your rotation handle to world (by using the rotation settings) and then change the rotation axis values (in the transform attributes) until your object lines up with your rotation handles. Kind of hard to explain, I think if you try it out, you'll understand.