It's really their own mess, in Classic, they basically stated: "Yeah, C'thun is dead, you killed some super power ancient being, gratz".
Blizzard also explained the Old gods imprisonment with the Titans that killing them would be too dangerous.
Then in Wotlk / Cata they started to throw curveball(s) with "They are outside the cycle", implying we are unable to truly kill them.
Deathwing, who has been empowered by the Old Gods, required DBZ Alphapowers to be annihilated out of existance, further supporting the theory from above.
Then came MoP with "Yeah, Y'shaarj got axe'd by some Mogu" (only to be retconned to Aman'thul himself killing him).
Then chronicle V1 came out and they basically went "Yeah, Old gods are just super massive void ticks".
The Old God lore is probably a good example that Blizzard lacks any sort of "lore bible" which they actually stick to that all presented plotpoints revealed over the course of multiple years still form a cohesive plot.
Fun fact, during the 4.1 PTR there was actually some early questchain in Silithus that C'thun actually returned, with his Eye spawning over Cenarion Hold.