Is repentance considered acceptable by returning a portion of ill-gotten money to the company that was stolen from and donating the rest to charities, or must the full amount be returned to the company?

You have committed several prohibitions: aiding thieves in unlawfully consuming people's wealth, remaining silent about evil, and unjustly acquiring money in exchange for your silence.

What is now incumbent upon you is: repenting to Allah, informing the company owner about the theft, and giving in charity the money you took in exchange for your silence to good causes. Your Hajj is valid and accepted, Allah willing.