This leads to some very bad behavior.
I'm wondering if we can come up with a solution to prevent this from happening, and hopefully pitch it as an enhancement to the Core team.
If it's alright to share, I have detailed the problem, and my thoughts on what to do about it on my blog, here: http://innerbot.com/wordpress-development/wordpress-needs-a-new-dependency-handler/
I'd like to be able to post a followup with some potential solutions/workarounds, but I'm still in the "figuring it all out" stage right now.
Anyone have any idea how to work around this issue?