As a work around I'm leaning towards a temporary solution in the form of linking /usr to the MicroSD card and that way it wouldn't fill up, doing it on a live system is tricky however, plus it seems the card doesn't get automounted on boot if it's not FAT.

Tried disabling the autogeneration of /etc/fstab from /etc/event.d/rcS-late and putting in the SD card, but it doesn't get mounted on boot...