A book is a great suggestion.
Understanding Exopsure, as mentioned above, has great reviews. I've never read it personally, but I've heard alot of great things about it.
Another book, that I have read, and would reccomend, is The Moment it Clicks, by Joe Mcnally. It's slightly more advanced, but it taught me alot. Understanding exposure, from what I've heard, is alot like a camera manual. Lots of great information, but boring and hard to digest. The Moment it Clicks on the other hand, has slightly less technical information, but it is a very entertaining book to read. Joe is an outstanding author (and a better photographer) who knows how to make his readers laugh. \
As far as equipment, yes, the stuff you mentioned has it's limitations, as others have pointed out. But it will take your wife months, if not years, to actually reach a point where she needs higher end stuff. I shot with my Nikon D40, and the Nikon equivalents of the same gear you are mentioning, for about 2 years before I finally reached a point where I NEEDED better equipment to advance my skill set.
I too, reccomend that you skip the filter. Yes, it could help an experienced photographer get better photos, but in all honesty for a beginner, it's just one more variable to have to worry about and adjust, and trust me, there are already enough of them built into the camera. More variables to deal with is a very bad thing when you are just starting out. Once she understands photography better, then the filter will be a good addition to her camera bag.