the script launched by cron should first check to see if the previous rsync is still running, if it is should simply exit.
You can perform the check using ps. If you have pgrep installed you might find that simpler.
Alternatively you could have your script create some sort of lock file, and then test for that. Here is a *very* basic example just to give you the idea.
if [ -f $lockfile ] ; then
rsync blah blah blah
rm -f $lockfile