Like @Robert_McKinney mentioned here: How to Remove/Unselect option in Multi-Select Custom Field using a Rule I too would love the option to have a rule do this for me.
Multi-select fields are a great way to keep track of which rules need to do what in a more complicated set of rules, to have the rules execute upon finding the corresponding field value.
Then clearing only that value after having executed the corresponding action is a great way to keep track of whether the rules are doing what they are supposed to be doing.
Currently one seems to need Flowsana to do this, or maybe it is possible with scripts.