If the hard drive is corrupt and cannot be repaired by Disk Utility, that really doesn't have anything to do with a virus, or any other kind of malware. That's a serious problem, and it is very likely, in fact, be an early sign that your hard drive is dying.
Regarding the malware issue, what makes you believe that you downloaded malware with a Flash update? Were you alerted to an "update" on a suspicious site, and did you install the resulting file? If so, you could have some kind of adware, or even potentially some kind of malware. In this case, you would probably want to revert to a backup prior to doing that. You don't need to worry about malware infecting the earlier backups... no Mac malware has ever been known to do that.