I believe they may just be keeping the vanilla Crysis branch going for this release due to possible bugs and stability issues with the Wars version that may require a bit more time to iron out. I wouldn't think the devs would want to keep 0.4.0 delayed for that long (after all they've worked long and hard on this and probably just as eager to release it to their adoring fanbase

).
Also it is a 'beta' so what better way to test the wars port than to let it loose for a bit. I do worry though like most of you that this will cause a split in the playerbase. I for one will keep both versions installed and up to date.
I predict 0.5.0 will be the end of the vanilla Crysis branch.
And yeah, we've been warned plenty of times that Wars was the direction the mod was going in, however it is a bit of a surprise that it's coming with the next release.