User blog comment:SayuriDarling/The Mark of Athena Official Discussion/@comment-5774152-20121214044606/@comment-3146930-20121214045432

It may be for another reason. The most obvious is that he is said to be the most powerful of the seven, but he is also unpredictable and can be hard to control. Someone like that is hard to plan for so your best bet is to capture them to get them out of the way and take out the smaller fish.

The other reason could be out of spite. Percy and Annabeth were the ones that lead Camp Half-Blood against Kronos and his army, eventually killing him. Kronos is her son after all and she may hold a grudge.