Technically, you are correct.
Practically however, the publisher may well be on the right side of this one (I haven't read the mod so I can only discuss the general principle).
If you want to advance a naga, the three ways that WotC provided that I remember off the top of my head are:
templates
HD
Class
Templates usually represent something odd about a creature or something odd that happened to it--god blooded, half dragon, half-fiend, zombie, etc. They grant a specific set of abilities. Obviously not what the designer was looking for.
Advancing by HD advances the combat capabilities and toughness of a creature but does not advance its spell like abilities very much. That's not very promising for a naga whose combat role is bound up in its magical and other special abilities.
Advancing by class is the last option and adds various abilities depending upon the class. Technically, it would only stack with creatures whose abilities exactly match class abilities. (So, a planetar cleric, for instance, would get more cleric spells). Creatures with spell like abilities just get the normal spells for the class. However, if you do that, it is hard to believe that adding one level of sorcerer to a creature that already has 3rd level spells as spell like abilities is going to increase its CR by 1. When is it going to use that clvl 1 magic missile or ray of enfeeblement? Only after it has used its better stuff and it'll probably be dead by then. So using that rule the way it is written renders the option useless in this case. The way that the authors appear to have done it seems balanced in principle as long as the creature ends up with spell like abilities that would be appropriate to a sorcerer of its CR (or slightly less given the non-magical abilities that a naga has--then again, less equipment and the commonly noted weakness of NPCs for their CR probably make up for this).