We resist renaming objects for many reasons and this issue is one of them. Choose wisely!! ;)
We have in excess of 150,000 objects and use Includes in virtually all of them and haven't found this restriction to be much of an impediment, just an annoyance.
When we are faced with a mass rename, our approach is to perform a "Search for use" with "Include Script" checked. We then Export the needed objects, use the appropriate utility or text editor to change the name and then Import the modified objects. For us this has been relatively painless and takes little effort.