You could write a wrapper shell script around rdiff-backup like this to start it:
#!/bin/bash
if [ -n pidof rdiff-backup ] ; then
kill -CONT $(pidof rdiff-backup)
else
rdiff-backup
fi
and then at 6 AM run a cron job with a script like this:
#!/bin/bash
if [ -n pidof rdiff-backup ] ; then
kill -STOP $(pidof rdiff-backup)
fi
The first script sees if rdiff-backup is running, and if it is, it uses kill to unpause it (if if is already unpaused, this has no effect/error), otherwise it just fires up rdiff-backup. The second script just sees if rdiff-backup is running, and if so, pauses it.