The sacrifice effect cards are only good if Progenitus is the only creature that they have out. And using non swords will just weaken every other match up. Depending on your build, the best way i see it is to preemptively stop it with discard. I have 4 thoughtseize main, 4 duress side. Against thresh put all that hand hate in and hope to keep natural order out. Also i have gaddock teeg in my side board which stops natural order from being cast.
Another way to stop him would be wing shard type cards. (hopefully he just attacks with Progenitus)

