I agree, a shell script might work. Something where you pipe the output of ls through awk and grep and sort ignoring "a" and "the". Another option might be to mangle the names so the old file name is something like "The Collection of Ants" and the new file name is something like "Collection of Ants, The".
The renaming is something that can be done in a shell script and then you'll see them sorted the way you want them in finder from now on.