Seeing a medical doctor and being checked for things like food allergies/intolerance, diabetes and hormone levels is advisable along with counseling. It is certainly a place to start.
There are also various herbs and other natural supplements that may help. I am not familiar enough with these to suggest anything in particular but I am sure some research online on your part will result in plenty of information.
There are many things that can be behind chronic depression, and it can be difficult to determine the exact reason or reasons. Situational depression is one that is very common where someone becomes depressed because of something to do with their life. Sometimes this can also mean environmental factors such as is common in Seasonal Affected Disorder (SAD) but can also tie in with the chemical imbalance issues.
Chemical imbalance, be it brain chemistry and/or body chemistry, is another very common reason. Sometimes these can be corrected with diet or other "natural" therapies. Sometimes though medications are truly needed.
I fully understand you and your wife's feelings about pharmaceutical treatments and think that by all means you should explore all other options first but at the same time I urge you to develop an open mind in regards to medications since the possibility is there that it could come down to it being your wife's only only option for a truly successful treatment of her depression.
If that option does eventually come to pass she will need your full support and encouragement to have any chance of accepting it. There really is no reason I can see at this point to discuss this with her. The only thing on this front I suggest doing is preparing yourself for that possibility.
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Moderator Depression Forum.