The whitelisting only applies to the "mobile" version of their browser. To that end, Microsoft's policy is markedly more Flash-friendly than what's happening on other Mobile platforms. After all, at least some Flash content will be permitted. By contrast, iOS and (as of recently) Android are effectively Flash-free platforms.
I think the fact that there's no restriction on desktop, combined with their published requirements for how to get whitelisted for mobile, make it pretty clear that this isn't really meant to be an attack on Flash. It's more an attempt to deal with the large number of websites whose Flash content is fundamentally incompatible with touchscreens because it assumes the presence of a mouse. Blocking Flash on those sites hopefully results in a better user experience because the site is theoretically degrading to a Flash-free version instead.
Far from being a Flash-killing move, in hindsight the other mobile platforms adopting a similar policy might have been the one thing that could have saved Flash for them.