Personally I'd probably use something to sync the lot over to a linux box and do the rest of the work from there. Depends on how much data you need to sync / how many servers are involved. Could be a pain to restore too (depending on the type of data you're backing up) so you would want to weigh all of that up too. With the Sql Server backups you could run periodic backups from Sql Server itself and have those backed up - depending on the data this could be really suboptimal but I think sql server allows incremental backups in the backup set, doesn't it? Been a number of years since I've had to deal with it.
You can use some sort of rsync alternative to get the content from the windows boxes to the linux machine (cwrsync is recommended - though I've never used it).
http://stackoverflow.com/questions/528298/rsync-for-windows
https://www.itefix.no/i2/cwrsync