Should I prevent my sister from speaking with a young man over the phone, knowing that she is very attached to him, or should I let her do as she pleases and disavow her action in my heart?

If your sister is speaking with this young man, this is a mistake, a sin, and leads to fitna (discord/temptation). You must denounce it with your hand, tongue, and heart. If you can prevent her with your hand without causing a greater harm, then do so. Denouncing with the heart alone is not sufficient when it's possible to denounce with the hand or tongue. Your sympathy for her because of her attachment to him is misplaced; rather, you should sympathize with her over the loss of her religion and honor. If the young man wishes to marry, he should propose to her. Otherwise, they should stay away from each other to avoid negative consequences.