The article linked by @Raja indicates:
I also announced that we were also working with SUSE and Fedora to bring their Linux distro’s to the Windows Store. Both SUSE and Fedora are nearing completion and will arrive in the store over the next week or two.
has some ominous wording in it (although probably only ominous because of its vagueness):
Q2) Should I continue to run the current/legacy distro or move to the new Store distros
A2) You can continue to run the current/legacy distro, but we do encourage you to move to using the store distro’s as your primary distro’s, because the current/legacy distro will be deprecated at some point.
They are not clear on what will be deprecated. It's probably the current bash on Windows stuff, but they don't say.
Edit: I got confirmation from Microsoft that what will be deprecated is the current Bash on Windows support.
Here is Ubuntu's announcement:
and some more background:
As @patdavid says, why not just jump ship to a good Linux distro?