The method you're using of assigning an alias IP address `bond0:0` is considered deprecated at this point with Linux kernels.
IP-Aliasing:
============
IP-aliases are an obsolete way to manage multiple IP-addresses/masks
per interface. Newer tools such as iproute2 support multiple
address/prefixes per interface, but aliases are still supported
for backwards compatibility.
An alias is formed by adding a colon and a string when running ifconfig.
This string is usually numeric, but this is not a must.
The correct syntax for deleting/downing an alias is to use `ifconfig` like so:
$ ifconfig bond0:0 down
I suspect you'd be able to do the same with iproute2's `ip` command as well:
$ ip link set bond0:0 down