I agree with seventy one about removing MacKeeper.
However, it does use a fairly decent anti-virus engine (licensed from Avira, unless that has changed recently). The issue of what to do with those malicious files is still present.
It's highly likely that all of those files are Windows malware that has somehow gotten onto your computer (attached to e-mail, perhaps), and from there into your backups. Knowing what names that malware was called would tell us for sure, if you are still in possession of that information. (If you have removed MacKeeper already, you are not.)
In any case, though, if the only malware on your machine was detected in the backups, and not on the system drive, you should be fine. Even Mac malware couldn't harm you if it was just sitting in your backups, unless you restored and then installed it.
As for deleting those files, sounds to me like you have manually put items from a Time Machine backup into the trash in the Finder, or MacKeeper has done that for you. That's extremely bad, and could possibly corrupt your backups. You should never touch Time Machine backups using anything other than Time Machine! For some help resolving this situation, see:
Can't empty the trash after deleting backups via the Finder
