It doesn't really matter which way you do it. HDMI through the receiver is the easiest way to wire things. The remote works only ONE way if you do things that way. It's an old arguement people put up which I disagree with: Your wife doesn't care about surround, but she probably would like to hear the news, or whatever show she watches, with the clearest sound possible, and that (in theory) is why you got the nice speakers and surround system - to not just get surround, but to get BETTER sound.
As such, if you want your wife to get good clear sound, she should be using the good speakers.
AS IT TURNS OUT... this is exactly what makes the system easiest to program as well.
You program the remote with one macro: "TV"
It turns the TV on, it turns on the receiver, it puts the TV on 'HDMI 1' input, and turns the receiver to 'TV' input (HDMI), and that's it. Press audio up and the recevier turns up, press audio down, and the receiver turns down. It is 100% transparent to your wife. I've had my receiver doing this for 5+ years and my wife, who could care less about surround sound, has not a single complaint because (as we discussed already) it's really easy and not at all confusing to anyone.
Unfortunately, it sounds like you want multiple remotes and to confuse the situation really by wiring things up so that the universal remote either must have two different TV macros - one with surround, one without. Or, that someone will use the TV/cable remote when they want to use the TV speakers, and will use the URC when they want to use surround.
I don't get it personally. Why buy decent gear, and a remote to make it work with one button press, then insist upon confusing things? If the remote is reliable it will be 99.9% effective everytime you press 'TV'. Everything will turn on and anyone in the family will hear TV just as they expect.
Not sure how to keep it simpler than that, and it definitely is not as simple running audio both ways unless you plan to manually use the surround system and simply leave the URC setup to turn on the TV and use the TV speakers for your wife/family.