Step by step !!,
We’re aware of the current use of non-free synthesis tools. But it dint mean, we're happy with.
So far the flashing process uses now free/open hardware and software, something that was not possible before.
The history don’t end here, there are very smart people working on some replacement for this missing free parts, but is Work In Progress, and requires more people to join and develop around it.

As in contrast the GNU compiler was no developed in a free/libre system from once. All require transition, and support, keep that mind :-)
If you are interested please join our irc channel #milkymist at freenode and tell us how you can help:

http://webchat.freenode.net/?randomnick=1&channels=milkymist

About the secrecy part i recommend you to read this interesting thread, worth take the time to read it, and scape from misinformation that is very common those days:
http://lists.en.qi-hardware.com/pipermail/discussion/2010-September/005369.html

You are right, Really Very few components from Opencores, actually Wishbone core is a modified version from the conbus core from opencores. But some cores developed by the main developer during the process, like the navre cpu and hpdmc controller we're published in opencores as well. Feel free to ask more questions here or at the IRC Channel at Freenode #milkymist also follow the development of the project by github A Quick Webchat link for IRC Chat here too: http://webchat.freenode.net/?randomnick=1&channels=milkymist

Or even boot the board choosing from different patched CPU's :-). Like a multi-boot option. That could be implemented as well with some development.

Please read the license from the Milkymist github repository: https://github.com/milkymist/milkymist/blob/master/LICENSE.LATTICE - "11. OPEN SOURCE SOFTWARE...."