Claire, I would think about seperating the wedding & the holiday planning rather than look at the whole thing being done by one tour operator which will limit your destination choice & do tend to include big fancy hotels.
There are many wedding planners actually in Greece, some deal with only a specific location, but some have quite a choice. Try looking at this one,
http://weddings.heliotopos.net/weddingshome.html
They seem to have a selection of destinations, all you have to do then is choose where, book your holiday, then get them to do the wedding package for you. That way you can choose the type of accommodation & location that suits you better.
Obviously this is not the only company, if you google 'Wedding planners in Greece' you should find plenty. Have a good browse & see who offers any destinations that interest you, or where you could get the ideal package holiday to, then research them by googling the names for reviews.
With the above company I notice they do Folegandros, Paros & Alonissos, all more traditional islands that would offer smaller accommodation in less crowded/touristy areas.
I would certainly consider booking flights & accommodation seperately too, to get the right location.