Hi,
I think it should not be so hard to implement the mapping – what about to have an array with simple “pairs” that would store the former column position and the actual column position? So when you update data, you would not put the data directly into the column of the specified order, but you would go through the mapping array and look for the current column position. No other changes in the code should be needed (except for updating of the mapping array after every column position change).
I would like to help with the implementation (to have it as soon as possible
) but I am quite new to JS so not able to implement the dragging logic :-(.
OT: With this enhancement, jqGrid would be the best grid component for jQuery (nowadays, if you need column dragging, you have to use flexiGrid). And since Microsoft has officially adopted jQuery for ASP.NET AJAX, probably many new users of jquery will come and it would be great to provide the best grid component, don't you think? 
hope we will figure out a solution
gius