This prophecy concerns the problems encountered in rebuilding of the Temple in Jerusalem. It is closely connected with the story in Ezra 4.
The wicked woman in the "eiphah" measure (bushel or barrel) represents one or more of the enemies of Israel, primarily the Samaritans and the Edomites, who harassed the builders after being excluded from the rebuilding project. Similar language of wickedness in Malachi 1:4. The eiphah is a standard dry measure and a symbol of justice. The word is used here to indicate that the iniquity of the enemies has reached full measure. This is a possible alliteration to the language of Genesis 15:16 [me].
The women angels in verse 9 possibly represent Judah and Benjamin (as in Ezra 4:1) or the Jerusalem and Samaria returnee communities who were rebuilding the Temple. In this prophecy they are removing the wicked from the land. They are the antitheses of the two women in Ezekiel 23:1 who brought wickedness into the land [Mordecai Zer-Kavod, Daat Mikra].
That there are angels in the form of women is according to Midrash Breishit Rabbah 21 (at the end) and Midrash Shmot Rabbah 25:2, also Maimonedes Guide to the Perplexed part I chapter 49, see also the Don Isaac Abarbanel on this verse.
The stork is a long-haul migratory bird with powerful wings. The power of the wings represents the stamina of the returnee community to deal with the harassment and send off their enemies far away. Similar Hebrew for the female forms with wings here in verse 9, clause 3 can be seen in Ezekiel 1:5-6 ("v'lhena c'nafayim"). The Hebrew here in verse 9 clause 2 is "v'ruah b'canfeihem", (with wind in their wings) where "ruah" can mean either wind or spirit. In this case the probable intent is "ruah hakodesh", the holy spirit, indicating that these women are indeed angels on a holy mission [A.S. Hartum, student of M.D. Cassuto].
The house for the wicked in the land of Shinar (Babylon) is saying that the enemies who are harassing the builders of the Temple in Jerusalem will eventually be worn out and will go back to build their own temples in their own lands. This probably refers to the Samaritans, who were exiled to Samaria by the Assyrians after the fall of the northern kingdom. The prophet is saying that these foreign implants will return to their former homes. In fact some did, but those who remained eventually built their own temple on mount Grizim. Mordecai Zer-Kavod posits that there is a parallel to Isaiah 49:17, "those who destroyed you will depart".
That is the simple meaning of the prophecy according to the approach of the ibn Ezra (1089 — 1164) that this particular prophecy was not escatological but like pre-exilic prophecy, was an interpretation of current events at the time of the prophet. (See Bernhard Anderson's Introduction to the Old Testament chapter 7 for an explanation of non-escatological prophecy.)
There is a difficult moral and religious dilemma behind this prophecy and Ezra 4. It is how to maintain the purity of the service of God and at the same time allow participation of non-Israelites. Should or could the returnee community have done more to allow non-Israelite participation? Or was it the case that the request to participate was a ruse or otherwise not sincere? Is this prophecy hinting that the returnees should pay off their enemies?