If you only want to do it on the server, you can access the raw mongo collection via a cursor, and then do the aggregation with the raw collection :
// collection is meteor collection
var collectionMongo = collection.find()._mongo.db.collection(collection._name);
collectionMongo['aggregate'](pipeline, cb)
haven't got very far implementing this but it worked basically on the server. On the client it might be more complicated since you have minimongo
Bit of a hack though, would be interested to see other ways of doing it...