No, it isn't.
Let me break this down for you:
GameFreak makes the game, not the anime. While it obviously has its hands in it, GF is a videogame company, thus the following point will be driven by logic as your question doesn't have any factuality behind it to hold it.
• The flagship Pokémon that were chosen for the first generation were Charizard and Venusaur, so to differentiate the two cartridges and ensure both a connection and a diversification between kids who played the games.
This happened in Japan during 1996.
• A year later, always in Japan, a Special edition, containing new sprites, was released and was called Blue.
During that year, specifically the 1st day of April in 1997, the pilot episode of the anime showcased in Japan.
• Five months later, on September 12th 1998, the Pokémon Yellow Version: Special Pikachu Edition was made accessible to the public due to the high popularity the show received.
Now, from this we should consider a few things:
As you said, Clefairy was meant to be the mascot for the anime, but due to its color and basic scheme design it was viewed as a bad marketing choice, for fear that it would only appeal to a female demographic.
Thus Pikachu who was, and still is, more neutral was deemed more appropriate, and in fact it appealed to both boys and girls.
Now in regard to the game, your question and my answer:
It couldn't be possible for the mascot to be anyone but Pikachu, since the game was based upon the anime as evidenced by the presence of Gary's Eevee, the Rocket duo with Meowth and the team they had in the anime and the unwillingness to evolve by Pikachu.
But this was for Pokémon Yellow, which was ONE game.
Game freak always releases two copies of the games, for socialization and lucrative purposes, so it wouldn't make sense for Pikachu to be the chosen one even before the first two games were released especially because it was an average electric Pokémon whom didn't stand out until it received a popularity boost thanks to the anime.
tl,dr: No, because it would create a Time-Paradox.
Got the links for you with the dates:
First Ep in Jap
Hopefully this will answer your question!