Might depend on if a Large Viper is "as bad" as a Huge Viper (relative to its Hit Dice) or worse.

Elder Serpent grants +2 Hit Dice. So a Large Viper would have 5 HD after the template is applied, and 3 HD before the template is applied.

So- before the template, it would have 3HD, and if the LA listed in the sample creature is an indication of the base race having -1 LA, (since the template itself has an LA of +3) - then the 3HD Viper would have an Effective Character Level of 2.

However- if the extra size between Huge and Large "counts" as raising the base race's LA, then the Large Viper might have an LA of -2 , compared to the Huge Viper's LA of -1.