"man modprobe.conf" lists blacklist as a valid directive. However, having any file in /etc/modules.d with "blacklist [modulename]" in it causes update-modules to error saying it couldn't create modprobe.conf:
modprobe: Invalid line 143 in /etc/modules.conf
Failed to to run modprobe. Giving up.
* Warning: could not generate /etc/modprobe.conf!
Not sure what's going on here.
Reopen if you still have this problem after you've moved your blacklisting stuff to /etc/modprobe.d/
I didn't initially have a /etc/modprobe.d but after creating it and putting blacklist stuff in there it does work correctly.