Most of the things you listed are issues with JIRA and Confluence, not the ASF's practices. Everything else on your list has already been fixed.
The ASF infra group did almost everything right but they still got burnt by esoteric details. The sshd conf had PasswordAuthentication set to no, but enabling PAM auth caused regular password auth to work. Did you know about that caveat?
And your top concern was that Slicehost didn't immediately shut down a machine?
tptacek never said that. He said it was a little disturbing that Slicehost took two days to turn off an instance that was exploiting a previously-unknown vulnerability in JIRA.
From the incident report https://blogs.apache.org/infra/entry/apache_org_04_09_2010 :
We notified Atlassian of the previously unreported XSS attack in JIRA and contacted SliceHost. Atlassian was responsive. Unfortunately, SliceHost did nothing and 2 days later, the very same virtual host (slice) attacked Atlassian directly. ( http://blogs.atlassian.com/news/2010/04/oh_man_what_a_day_an... )
Apache's infrastructure group got their shit together quickly. The hacked Slicehost instance wasn't a threat to them anymore. Slicehost's inaction helped get Atlassian hacked, which I think is a bit disturbing.
Would it have really slowed the hackers down for more than an hour anyway?
Oh, you're right. Let's just leave hacked systems running. Shutting them down will only slow down hackers for an hour.