Since we're talking about Time Machine, if it was me I'd only have the external drive backed up when it's connected to the Mac it's usually connected to. I know this isn't really what you're asking, but I believe it to be your safest option (mainly because it's simpler and you've got less room for human error). And, from my experience, external hard drives usually find themselves connected to one machine more than others.
However, if you find that the external drive is regularly connected to either Mac for prolonged periods and you're really needing it to be backed up regardless of the Mac it's connected to, then your terribly inelegant solution is really the only way to go. If so, you may want to rethink your file structure so that it's easy to "split" the contents being backup up by each respective Mac. (Assuming, of course, it's not already easy to split things up).
For example, you could split your media files into two main folders (one for backing up via the MacBook Pro and the other by the MacBook Air). Of course, these folders may have any number of subfolders.
Another example could be that all files are grouped into folders labelled as 0-9, A-M and N-Z (or whatever works for you).
Regardless, the idea is to make it easy for you to split them up within your Time Machine settings so that it's very clear which one(s) are backed up by one Mac, and which ones are backed up by the other Mac. Then you just keep organising your files within these folders as you need.