I wouldn't say undermining the happy ending of the game is a flaw of the theory in of itself.

That being said I don't think a tragic subtext to the love story is how SE intended it to be interpreted. The reasons that make this theory implausible have been enumerated countless times and don't need to be repeated here.

What I will say is that anyone who wants me to accept it must furnish convincing arguments. It is not the role of skeptics to prove a negative. So far the arguments in favor have not been persuasive.