In the FAQ section, we address basic concerns like What is a UK EEA Family Permit? & ILR.

You should also consult the UK Border Agency which provides information on supporting evidence for EEA Family Permit. They list required documents as :
" a copy of the EEA national's passport, endorsed by the EEA national's embassy in the country of application); and
proof of your relationship to the EEA national (for example, your birth certificate or marriage certificate); and
a letter from the EEA national, declaring that you are travelling with them or are joining them in the UK."

Where are you finding the info about sending the original passport?

 

Your wife will have to send her passport in, as the Home Office will have nowhere to put the endorsement stamp/sticker except in a passport. You being the EEA national, only a copy of your passport is required as getting verification of its authenticity will be easier and more feasible here in Europe than a non-EU national passport.

Make sure though that all the documents and passport are sent via a trackable service, and most will have some form of insurance as part of the fee in case the documents are lost in transit.