We had a user leave our company who had a BB. Her user account in windows and her mailbox were already deleted so i can't take her account off of the BES server cuz BB Management server says it can't access her mailbox (obviously).. is there a way to delete the user from the BES forcefully or thru a command line?

try the besadminuserclient from the resource kit there is a -delete option

havent tried it though so not sure it will work.

When I try to remove a user whose mailbox is inaccessible, I just choose the option to not remove the Blackberry Information from their mailbox and it removes them.

Assuming you are on BES 3.6, upgrade to the latest service pack and try again. After a certain SP level on 3.6, this was corrected (SP4, maybe?).