The bonus language granted by the Tongues curse is added to the languages you know, not the languages you can choose to know by virtue of high intelligence. Here's why:
You apply your character's Intelligence modifier to:
- The number of bonus languages your character knows at the start of the game."
Note the wording: Bonus languages are languages your character knows at the start of the game, not a list of languages they could potentially know. Here's another quote, this time from the races section of the PRD:
Languages: Dwarves begin play speaking Common and Dwarven. Dwarves with high Intelligence scores can choose from the following: Giant, Gnome, Goblin, Orc, Terran, and Undercommon.
The reason why this quote is significant? Those languages aren't described as "bonus languages." Again, this is because "bonus languages" are languages a character knows as a bonus of having high intelligence, not languages they could potentially know.
Incidentally, if you don't gain the language, it's not really a bonus. That'd be like calling "elf" a "bonus race" for your dwarf character because it's an option you could have taken.