Depending on how pymongo uses the dictionary, you might be able to use OrderedDict (from the builtin collections module). This is only available from python 2.7, but there are backports available for python 2.4 onwards.
In this case you could do something like:
from collections import OrderedDict
config = OrderedDict((
("cloneCollection", "db_name.collection_name"),
("from", "localhost:27017"),
))
db.command(config)