Ah, I love a good conspiracy theory!
So, let me get this straight. People believe that Toyota manufactured the result in both a highly obvious way, and with an amateurish stunt?
It seems to me, that if your goal was to achieve a better marketing outcome (Alonso's car winning) you would do it in a clandestine way, not this wacky races stuff. If their desire was to fix the race, then there were likely 100s of better ways of doing it. For me, Occam's Razor shuts down the "it's a fix" line of thinking pretty quickly. But, externally, there's a lot more to think about...
If Toyota were to be discovered to be fixing races, the reputational damage would far outweigh any positive marketing outcome from the WEC project. But, more than that, it would taint any goodwill towards the brand from even the most casual observers, just ask Lance Armstrong.
For me, the marketing return for the #8 car winning instead of the #7 would be small, but noticeable. After all, #8 won last year, and the Championship, it's not as if they were short of marketable stories. But, there's also an argument that both cars being winners of the big race would be better from a marketing perspective. Mercedes certainly made good use of that when Rosberg picked up the title in 2016.
But, all of that is just hypothesising. The fact is that the positives of an Alonso win would be massively outweighed by the risk of being discovered. And, that's not even touching on any legal repercussions.
Finally, this falls down in the same way every conspiracy theory falls down. It requires far too many people to be in on it, and to stay quiet.