Instead of deleting the group objects, you can just set the association of employee to group(s) as empty in the microflow and then the employee object will no longer be associated to the group(s) that were previously assigned.
You would just need to use a change object action and the association should look something like $Employee_Group then set that reference attribute to empty in the change action.
Aaron,
In a change Action, you should select the reference set and click Remove. Then you can place the list of objects you want to remove from the reference set in the Value box. The screen shot below demonstrates this:
Hope that helps,
Mike