A launch for a client also went through the same problem in 2010, and that was after 5 years of managing other WP installs (including 2 VIP WP sites). I've seen it happen too many times for it not to be Automattic's problem to address more so than they're doing now.
Stay away from self hosted WP unless your install is absolutely bullet proof, and cross linking, especially to resource files from other WP sites is the last thing you should ever do because you do not control their security which can directly affect yours, or at least your black list vulnerability due to associated content.
Our office used to be above Automattic's in SF, and I love those guys, and what Matt has done for the web, but with great power comes with great responsibility.