Actually, both endings are flawed. If the movie had kept the squid, half the audience would've been like WTF!? But, since they changed it, it creates a major plot hole: Why do they stop fighting if Dr. Manhattan (who they blame instead of aliens in the movie) is in a flippin' other galaxy?
"Life and death are unquantifiable abstracts. A live body and a dead body contain the same number of particles. Structurally there's no discernible difference."
Wait, how did Bobby get there? Prof. X said they should only bring their most experienced students, and he wasn't there when they went into the tomb!