You could still keep a record of all calls made, and the tower(s) used to make each call, without getting down to this level of granularity. I might be wrong here, but it seems that they're storing a stream of triangulated location data for a given handset, regardless of the actual network activity like calling.

Let's say that the carriers only stored call records with tower IDs for each call. If there was a dispute every so often because a call was made on a close-by tower that itself happened to be located in a different toll bracket (resulting in an incorrect overcharge to the customer), I'm sure the carrier would happily write off that charge if you disputed them about it, which is probably what they'd do right now anyway.

There must be another reason they're keeping it, even if it's just a case of it being super-cheap to store, and they think that they might figure out something to do with it later.