I once let Google crawl an alternative hostname for ~2 hours and it took more than 6 months for the damage to be repaired.
Once Google has spidered the data it's very difficult to get it altered.
Denoting the links as "via" is the same situation I ended up with. It does eventually sort itself out.
Two years on, there's still a few remnants of the effects of that upload-the-wrong-htaccess-file disaster to be found in the reports, but most of it has been fixed.