Sounds like more work than its worth.
Putting the infrastructure in place to filter files sounds like it'd be more time/effort/cost than just sucking it up and buying more disks and bandwidth. Especially since, like all backup services, they charge per gigabyte / TB. Mass storage, especially of the performance level you'd expect for backups, is ridiculously cheap nowadays, you can get disks at less than 3 cents per gigabyte and you can get a 90-bay JBOD chassis for about $10-15k. Bandwidth is fairly cheap too.