In Michael Cacoyannis 1977 film Iphigenia, made in Greece with an all-Greek cast, the name was pronounced throughout as If-i-GAYN-ya. I think that’s the prettiest pronunciation.
This is such a gorgeous name - for a fictional person, anyway. I really can't see an Iphigenia walking around without a good, solid nickname - maybe call her by her middle name, since nicknaming options are scarce here.
It's admittedly quite an interesting name, and it doesn't sound far too pompous, megalomaniacal, or foreign, but it might lead to bad nicknames like Iffy and Genie. It also sounds a bit elitist, but I suppose some might say the same about the gorgeous Phaedra, even though it's much simpler. I wouldn't talk you out of it.