The issue with the certificate downloading without the class being finished is a grade book setting issue.
I am pretty sure that trying to use scorm as a conditional activity is not supported at this point but there are work around for that like making the scorm give the password to a short quiz then make the quiz the condition not the scorm. I could be wrong on this. I remember reading SCORM program should be set with a grading method other than 'learning objects' to report a score. If the grading method does not work a single question true false quiz will.
Take a look at http://moodle.org/mod/forum/discuss.php?d=119925, into the gradebook demo 3 you can see how to get your weights and aggregation. Play with the setting and see what it does to course totals and you'll get it right.