Or a field schema_version that's increased with each installed patch?
I was thinking along the same lines, but something a bit more general. A site_props table, with key-value pairs. It would be like objectcache but guaranteed persistent, and it could be used to hold things such as a boolean value showing when the update in question is applied.
I prefer that idea. A version number requires that patches be installed in a particular order, which could cause problems (especially if 2 patches are being developed simultaneously). I don't think a boolean value would be required - just the existence of the row would be enough.