Hi @Joel Nave,
You have to do this by Bulk Feature. First, run a filter for the label you want to remove then using the Bulk Change feature, Edit the selected tasks. I am using JIRA 7.1 but your screen should look similar to the following:
Keep in mind that you have to fully remove the unwanted label from all tasks for it to disappear from the list when typing the label.
Hope this helps!
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