A Timestamp Value is converted to BSON as a long long:

        case Timestamp:
            pBuilder->append((long long)getTimestamp());
            break;

Test

c = db.c;
c.drop();

c.save( { a:new Timestamp( 0, 0 ) } );
assert.eq( c.findOne().a, c.aggregate( { $sort:{ _id:1 } } ).result[ 0 ].a );

Observed behavior: A timestamp field is converted to a long long in the aggregate command's output.
Expected behavior: A timestamp field remains of timestamp type in the aggregate command's output.