So what you're telling me is that we have 2 possible scnearioes.
1) Sheperd is now, officially dead. He is beyond the council. He is beyond the Alliance. He is a tale told to dissobidient geth children to make them eat their greens. Yet he still walks the battlefield as one of the most terrfiying pieces of psychological warfare in history...
2) Or 40 hours of my life, the only 40 hours of heroism, awesome and cheer badassery, has just been martyred.
Either way, I'm glad. There's nowhere to take your level 50 juggernaught if you carry on the character. And they could hardly pull a Link on him and just dump him somewhere with a poorly written justification as to where his uber gear and biotic/tech/murder prowess has gone. Playing as, say, the 4th human spectre, thanks to the efforts of Sheperd and humanity's place on the council, could be awesome. You could even work with the other spectres, planning things with them to gain benefits on some plot missions. Imagine Feros where another agent took over one of the AA cannons and held it long enough to take out any geth dropships that show up or provide overkill fire support. Then have another option where they don't comandeer, they just destroy each one of them and you dive in with the Normandy, cutting out that AWFUL Mako section.