There is no current means to directly deactivate an entire submechanism from the parent model.
Solution
Change to the submechanism and create a new Solution. Once the new Solution is active, use a multiple select to highlight all of the motion bodies and then right-click on the group. Select "Deactivate" in order to set the motion bodies and all of the referencing elements to inactive. NOTE: it is very important that "Deactivate" is selected and NOT "Deactivate for All". The former will deactivate all of the elements for the new Solution only, while the latter will deactivate all of the elements for all existing Solutions. This will make it difficult to reactivate the submechanism and render it useless on its own.
Notes