Well the way you put it, it's going to be hard to match because there is nothing in there. But in the real world you would probably try to match like this:
db.t.update(
{ "_id": "53296f43630a817c1af2a3e8" },
{ "$pull": { "pages": { "value": 1 } }
)
That is assuming that there is a "value" property in the "sub-document".
But if you really do mean something like this where the is nothing to match, then try this:
db.t.update(
{ "_id": "53296f43630a817c1af2a3e8" },
{ "$set": { "pages.1": false } }
);
db.t.update(
{ "_id": "53296f43630a817c1af2a3e8" },
{ "$pull": { "pages": false } }
)
Which sets a value you can match and then matches and removes it.