cómo actualizar el número de secuencia en mongodb de forma segura

Para hacer esto de manera atómica, los tres documentos de muestra deben ser parte del mismo documento. MongoDB solo realiza operaciones atómicamente en documentos simples:http://www.mongodb.org/ display/DOCS/Atómica+Operaciones

Si son parte de un solo documento, lo siguiente cambiaría el orden del 2do y 3er subdocumento:

> db.so.find().pretty();
{
    "_id" : ObjectId("4f55e7ba362e2f2a734c92f8"),
    "subs" : [
        {
            "author_id" : "a",
            "class" : "principle",
            "content_id" : null,
            "host_id" : null,
            "modified_date" : 1330935540,
            "order" : 1,
            "pub_date" : 1330935540,
            "score" : 0,
            "text" : "Hello World！",
            "vote_down_count" : 0,
            "vote_up_count" : 0
        },
        {
            "author_id" : "a",
            "class" : "principle",
            "content_id" : null,
            "host_id" : null,
            "modified_date" : 1330935538,
            "order" : 2,
            "pub_date" : 1330935538,
            "score" : 0,
            "text" : "Nice to meet you.",
            "vote_down_count" : 0,
            "vote_up_count" : 0
        },
        {
            "author_id" : "a",
            "class" : "principle",
            "content_id" : null,
            "host_id" : null,
            "modified_date" : 1330935548,
            "order" : 3,
            "pub_date" : 1330935548,
            "score" : 0,
            "text" : "Great!",
            "vote_down_count" : 0,
            "vote_up_count" : 0
        }
    ]
}

Consulta:

db.so.update(
    { _id: new ObjectId("4f55e7ba362e2f2a734c92f8")},
    { $set : { 'subs.1.order' : 3, 'subs.2.order' : 2 } }
);

Resultado:

> db.so.find().pretty();
{
    "_id" : ObjectId("4f55e7ba362e2f2a734c92f8"),
    "subs" : [
        {
            "author_id" : "a",
            "class" : "principle",
            "content_id" : null,
            "host_id" : null,
            "modified_date" : 1330935540,
            "order" : 1,
            "pub_date" : 1330935540,
            "score" : 0,
            "text" : "Hello World！",
            "vote_down_count" : 0,
            "vote_up_count" : 0
        },
        {
            "author_id" : "a",
            "class" : "principle",
            "content_id" : null,
            "host_id" : null,
            "modified_date" : 1330935538,
            "order" : 3,
            "pub_date" : 1330935538,
            "score" : 0,
            "text" : "Nice to meet you.",
            "vote_down_count" : 0,
            "vote_up_count" : 0
        },
        {
            "author_id" : "a",
            "class" : "principle",
            "content_id" : null,
            "host_id" : null,
            "modified_date" : 1330935548,
            "order" : 2,
            "pub_date" : 1330935548,
            "score" : 0,
            "text" : "Great!",
            "vote_down_count" : 0,
            "vote_up_count" : 0
        }
    ]
}