There are software packages out that watch files that are being touched and scan them for known matches, viruses, etc and can quarantine them. Also software that watches out for relaying of emails and scripts sending out a ton of email (spam). A decent shared hosting company already does these two things. Common practice would be to disable the malicious code if it's still there (a lot of bots upload, execute, then remove the files) or reset compromised passwords and notify customers of what's going on. Let the customers deal with their own stuff. It's way to messy to force these types of upgrades on them, with the exception of maybe known exploits - like automatically replacing outdated timthumb.php code.

While I love S3, its not for the common person. If Google used an S3-style system as a good backbone and added a few very usable features it would be an improvement. I like the power of writing my own scripts and controlling what I send to S3, but I'd like to have more power to see what is in my buckets. I can do list command, but I'd like to know sizes and dates and to be able to query that information easily. Even just view it in a web control panel just to grab a small file from it.