The file prefix is very handy. Sure it doesn't work in burst mode but that's what warnings are for.
Processing 2000+ wedding photos, it's much easier to pick out the dual ISO shots with the prefix then to wait hours batch processing the lot of them.
It's only a problem where you have alternate shooting enabled. I'd settle for reduced capture rate where file prefix is not default and alternate capture is enabled.
I've made a short benchmark for 20 non-dual-iso cr2 files using cr2hdr alone and scripts I have there:
http://www.magiclantern.fm/forum/index.php?topic=8738.msg81768#msg81768cr2hdr alone (drag&drop) = 1:46.52
No renaming of files, just many processes of cr2hdr:
timer cmd /c dualisonorename.vbs = 48.391 (maxprocs=4)
40.902 (maxprocs=8 ) 41.252 (maxprocs=16)
Many processes of cr2hdr + renaming using exiftools:
timer cmd /c dualiso.vbs = 59.851 (maxprocs=4) 62.404 (maxprocs=8 )
So for 2000 photos it would take 1 hour 8 minutes on my old computer (Core2 Q6600). Less than that, because the program takes some time to start and stop (less processes at once then). Of course, for Dual-ISO files the time will increase, but so as with your method.
And I think I have some photos with wrongly assinged prefix that were not made by burst but by Always On AETTR. Probably ML finished calculations of new exposure at the exact moment I took the photo?