Can I track single emails with CiviCampaign?
You're correct; the email UI (user interface) doesn't allow you to specify a campaign. However, the underlying database table is civicrm_activity, which DOES support storing an associated campaign.

You could write an extension (or hire someone to write an extension) that adds this functionality to CiviCRM, and because the underlying table supports what you're doing, it's relatively little work.