カスタムを使用してConverter、そのインターフェースのタイプを逆シリアル化する方法をJSON.NETに指示できます。以下のコードは例を示しています。
public class StackOverflow_12197892
{
    public class Data
    {
        public IEnumerable<IChild> Children { get; set; }
        public override string ToString()
        {
            return string.Format("Data{{Children=[{0}]}}",
                string.Join(", ", Children.Select(c => string.Format("{0}/{1}", c.Name, c.IsFemale ? "girl" : "boy"))));
        }
    }
    public interface IChild
    {
        string Name { get; }
        bool IsFemale { get; }
    }
    public class Son : IChild
    {
        public Son(string name)
        {
            this.Name = name;
        }
        public string Name { get; private set; }
        public bool IsFemale { get { return false; } }
    }
    public class Daughter : IChild
    {
        public Daughter(string name)
        {
            this.Name = name;
        }
        public string Name { get; private set; }
        public bool IsFemale { get { return true; } }
    }
    class ChildConverter : Newtonsoft.Json.JsonConverter
    {
        public override bool CanConvert(Type objectType)
        {
            return typeof(IChild).IsAssignableFrom(objectType);
        }
        public override object ReadJson(Newtonsoft.Json.JsonReader reader, Type objectType, object existingValue, Newtonsoft.Json.JsonSerializer serializer)
        {
            JObject obj = serializer.Deserialize<JToken>(reader) as JObject;
            if (obj != null)
            {
                bool isFemale = obj["isFemale"].ToObject<bool>();
                string name = obj["name"].ToObject<string>();
                if (isFemale)
                {
                    return new Daughter(name);
                }
                else
                {
                    return new Son(name);
                }
            }
            else
            {
                return null;
            }
        }
        public override void WriteJson(Newtonsoft.Json.JsonWriter writer, object value, Newtonsoft.Json.JsonSerializer serializer)
        {
            throw new NotImplementedException();
        }
    }
    public static void Test()
    {
        Newtonsoft.Json.JsonSerializer serializer = new Newtonsoft.Json.JsonSerializer();
        serializer.Converters.Add(new ChildConverter());
        string json = "{'Children':[{'name':'John',isFemale:false},{'name':'Mary',isFemale:true}]}".Replace('\'', '\"');
        var obj = serializer.Deserialize(new StringReader(json), typeof(Data));
        Console.WriteLine(obj);
    }
}