I don't think that's what is happening here.
Uprising was indeed supposed to come out before Halo 3 but ran into publishing issues between Marvel, Bungie, and Microsoft. I imagine 343 Industries won't have that problem now that everything Halo is managed from one location (and they're more prepared for publishing-related duties than Bungie was).
There is no indication that Kilo-Five Book Three has been delayed like Uprising was.
I'd guess The Thursday War sets up for Halo 4 while Book Three deals with the immediate aftermath, but that's pure speculation. Even if Book Three takes place before Halo 4 there shouldn't be any plot issues because Karen Traviss and 343 knew so well in advance.