One solution adopted in other applications that would work here is a popup window with a list of all child thoughts. Then one could drag individual thoughts up or down this list until they were in the right position. Then close the window.
In addition to this I would also like to see thoughts arranged by Link Type, particularly children of the active thought. This could be another way of arranging thoughts, e.g., by having a set of links named "1", "2", etc., although this would not be a very efficient way of REarranging thoughts, since every numbered link type would have to be re-typed to accommodate a new child.