Since this thread is Speculation based upon Spoilers, then here's my view with some SPOILERS added in.
According to Spoilerfix.com, [....spoiler]...Michael Vartan is back for episode seven. He'll supposedly make another guest appearance in the 9th episode. With this new intel, I must say...it definitely doesn't look like MV is dead.
If MV isn't dead, I personally think that Jack and the APO team extracted him. Syd gave him the water before he coded out...maybe she didn't know...it looked like she didn't...but who knows? My money is on the grandpa. Now on what condition he's in or where he's at is a mind teaser...if Jack is in on it, then there's no telling where he's at. I think Jack is hiding him in plain site...in France (because he's french) or right there in Los Angles (because nobody would expect it).
If VM is dead, then it's sad. However, the show has progressed forward smoothly and nicely...just like the good ol' days of Alias. With his guest appearances, though, one could conclude that he's here for flashbacks with his time with Renee' or I've heard dream sequences (but i hope it's not true).
Thanks for reading my chit chat!