Given the differences between you and your wife, I’d recommend either creating your own curriculum (picking and choosing depending on the subject), or choosing one that allows you the flexibility to substitute subjects out as you please.
Every Catholic homeschool program will have a strong faith component. I understand your hesitance with Seton. It is an excellent program, but even as a Catholic, I have been a little put off by the titles of the history texts not sounding very comprehensive and the “…for young Catholics” in the title of all of their texts (I actually use several of the texts, so I’m really just complaining about the titles). Not for the same reasons as your wife probably, but I do agree that their style will probably not appeal to many non-Catholics, at least not those who are sensitive about religious differences.
I have used Kolbe Academy, which is just as faithful theologically, but which probably doesn’t give off the same in-your-face-Catholic first impression that Seton might to a non-Catholic person. For one thing, they use a lot of secular texts, in many of their subjects. Much of their literature is not specifically Catholic, but just good Classic literature. They use secular materials when those are the materials they think teach the subjects the best (such as their math programs). But they don’t include anti-Catholic secular materials and their lesson plans enable you to add the Catholic perspective. One thing Kolbe does really well is science - they use secular science texts and insert the religious perspective only where needed. Now depending on your wife’s views, those perspectives may or may not be acceptable to her. Kolbe does not teach “young earth” science as many evangelical texts do. In their lesson plans, they direct the parent to resources and explain that while there are certain factors that MUST be true about the origins of human life (such has all humans having the common ancestors of Adam and Eve, and God giving them their human soul), the Church has not proclaimed whether the earth was created in a literal 6 day timeframe or whether God gave us the process of evolution by which the earth and its creatures progressed. In other words, what the Church officially teaches about evolution.
The other plug I’ll make for Kolbe is their flexibility. If you decide to homeschool with them, they will give you all of the lesson plans for the courses they suggest, but they are totally ok with you using different curriculum for any (or even all) subjects. So if you like much of what they use, but want to substitute a different history text, you are free to do so.
I would suggest looking at the Kolbe Curriculum as well as that of Mother of Divine Grace and Angelicum Academy, and just see what materials appeal to you. Interestingly, if your wife is of the evangelical style that prefers the young-earth philosophy, she might actually like Seton for science, as Seton uses Apologia for at least some of their science (Apologia is protestant).
Memoria Press is a wonderful Christian publisher. I hear that they are not any one denomination, but that they are Catholic Friendly. They started out as mostly a Latin curriculum provider, but I believe the offer a more comprehensive curriculum now. I would also recommend looking at their materials.
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