You absolutely do NOT want to redirect these links to the home page, Ian! These are spam links, coming from completely unrelated sites. They are Google's very definition of unnatural links and 301-redirecting them to your home page also redirects their potential damage to your home page.
You want them to return 404 status as quickly as possible. I'd also be tempted to use the Webmaster Tools remove tool to try to speed up the process, especially if these junk links currently form a large percentage of your overall link profile. (You'll need to find & remove the redirect that currently re-points them to the home page too, for the 404 header to do it's job of telling the search engines to drop the page from their indexes.)
As far as rankings issues, this isn't a potential dupe content issue, it's a damaging unnatural links issue, which is even more significant. These are the kinds of links that could lead to at least algorithmic penalty, or worst case, manual penalty. Either way, these penalties are vastly harder to fix after the fact than to avoid them in the first place.
In addition to the steps above designed to make it clear those links don't belong to your site, I'd keep a good record of the links, their originating domains, and when & how they were originally created due to the malware attack and your fix. That way you have essential documentation should you receive a penalty and need to submit a reinclusion request.
Hope that answers your questions?
Paul