Rewrite the sentence to make the pronoun reference clear.

she traced her ancestry back to the original president of the college, which her roommate thought was unfair.

the answer to your question would be that to make the pronoun reference clear another version of the sentence would be the following one: her roommate thought that it was unfair that her ancestors traced back to the original president of the college.

what the sentence really means is that her roommate considered unfair the fact that she was related to the first president of the college.

where is the