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Yeah, your options involving DNS are severely limited. Really, you have to have a web server send the proper codes (in your host's case they're using their own). So point them to your server and have it return the 301s you need.

Thanks Highland and Donnie for your input. It's not a sitewide, though there are three links from it. AVG's tool confirms the threat so it's definitely a bad seed (thx for the link). I know it's not that bad and that link alone can't penalize the website I work with, but that one gives me a lot of work : borderline spammy profile, with two "satellite site" heavily linking to it that were penalized (because of abuse of anchor text precisely)... not quite natural, though itself wasn't penalised by Penguin. I guess old numerous triangle links between the same webmaster's websites aren't triggering the algo, even if they're penalized, but I prefer to do a little bit of cleaning now before it's too late^^

Yeah, normally I'd say to NOINDEX those user-generated search URLs, but since they're collecting traffic, I'd have to side with Alan - a canonical may be your best bet here. Technically, they aren't "true" duplicates, but you don't want the 1K pages in the index, you don't want to lose the traffic (which NOINDEX would do), and you don't want to kill those pages for users (which a 301 would do). Only thing I'd add is that, if some of these pages are generating most of the traffic (e.g. 10 pages = 90% of the traffic for these internal searches), you might want to make those permanent pages, like categories in your site architecture, and then 301 the custom URLs to those permanent pages.

Sorry you're stuck in that spot. I really would be worried that this "fix" would make life worse for everyone, but it's tough to come up with solutions that don't seem like band-aids. Best you may be able to do is get more aggressive about the de-indexation, focus on improving some core content, and maybe re-work the internal linking to focus more on key pages (and spread internal PR a bit less thinly).