The answer to whether Elizabeth made a rational decision in refusing Mr. Collins in Austen's Pride and Prejudice all depends upon from whose perspective you are asking. From Mrs. Bennet's perspective, Elizabeth's decision was not a rational one. Though she is rightly criticized for her foolish behavior, Mrs. Bennet does express some sound reasoning of her own, which is confirmed by Charlotte Lucas's choice and her explanation to Elizabeth.
Mrs. Bennet is anxious her daughters to marry, and marry well, because she rightly holds that a young woman without wealth of her own has no hope for a home of her own, other than her father's home, unless she marries; and she can have no hope for social privilege or the independence of a comfortable life unless she marries a man of wealth. These are precisely the reasons that level-headed, unromantic Charlotte chose to marry Collins herself:
marriage had always been [Charlotte's] object; it was the only provision for well-educated young women of small fortune, and ... must be their pleasantest preservative from want.
"I ask only a comfortable home; and considering Mr. Collins's character, connection, and situation in life, I am convinced that my chance of happiness with him ...."
From Elizabeth's perspective--which was shared by Jane--Elizabeth's decision was absolutely rational. For Elizabeth, marriage was inseparable from respect, esteem, amiability, and love. To even think of marrying without these, especially without love, was impossible. After hearing of Charlotte's loveless engagement ("Mr. Collins ... was neither sensible nor agreeable; his society was irksome, and his attachment ... must be imaginary."), Elizabeth could only understand it in the most mercenary terms, those of sacrificing love for material gain:
[Elizabeth] had not supposed it to be possible that, when called into action, [Charlotte] would have sacrificed every better feeling to worldly advantage. ... it [must be] impossible for that friend to be tolerably happy ....
Mr. Collins was not only unloved, he was, in Elizabeth's eyes, impossible to love and, worse yet, impossible to esteem and respect because he was not a sensible or wise person--he was as foolish as Mrs. Bennet--and had no great beauty to make up for it! For Elizabeth, it was completely rational to choose to refuse Mr. Collins's offer of marriage, indeed, it would have impossible to do otherwise. Jane understood this as completely as Elizabeth failed to understand Charlotte's choice to marry him.