Holy freaking cow!
Now, this really approached Evangelion-level of mindfuck with gigantic Father and everyone dying stuff.
I totally didn't expected that Father's plan would go as far into successful territory as it just went. I thought that Hohenheim's or Ishvalan countermeasures would kick in leaving Father in a "WTF? Why did my plan not work?" state, but Arakawa slapped another cliffhanger in our faces. Damn, why it's a monthly series ;/
I do personally think that yes, they are indeed dead, but since their souls are being held inside Father (and not departed like it was for e.g with Trisha) most probably Ed & co. will find a way to bring them back into their bodies. But they need to hurry, before the bodies will be damaged irreparably from, you know, being dead.
And I'm not so sure that even if they succeed we'll see everyone back safe and sound, since this binding-the-Truth-down business is probably very soul-hungry...