I think the two of you need to think out what, realistically, the chances are of things happening that could leave you without enough gear; that may help you decide how far you really need to take the idea of doubling up. (Personally, I'd be more worried about someone stealing my pack if I left it outside a store, or leaning against a tree while I took a sidetrip.) The mere process of thinking this stuff through may help ease some of her concerns.

"Thinking out" does NOT mean laughing at her fears or telling her she's nuts - though they may seem silly to you, this is obviously a serious concern to her; and serious concerns, real or imagined, can heavily affect one's enjoyment of a trip.

I can think of a couple of things, if you do decide to duplicate gear. These things will probably add weight to your total load, so the two of you need to consider that. You may determine that the extra weight is a small price to pay to alleviate a concern you've rated more highly, or you may decide that it's too heavy for the low risk it addresses. Either way, it's your decision and it's valid - no one's going to be at the trailhead to weigh your packs and give you bonus points for being the lightest pack of the day, or telling you that you can't hike on because you've exceeded the weight limit.

I'm assuming you carry a supply of purification tablets in case your filter breaks. (I do, even though it never has - my own concern showing.) If you do have both, one of you could carry the filter and the other the tablets. That way, you both have a way to purify water.

How many pots are you carrying? Are you carrying metal mugs? As long as you're carrying two things (2 pots, 1 pot and 1 mug, etc.), you can split them up so both of you have a way to do at least minimal cooking. If you have a stove, then make sure whoever isn't carrying it is carrying some sort of firestarter (a spare lighter/matches); that person can always cook over a fire.

Each person carrying a pocket knife, map, toilet paper, and compass is always a good idea, in my book. Likewise, if I'm sharing gear, I make sure the person who isn't carrying the main first aid kit still has a minimal first aid kit (bandaids, advil/tylenol, moleskin, Neosporin, and a couple of safety pins.)

As far as shelter, I'm not sure I'd divvy up the tent - without the poles, it's a lot harder to pitch either the inner or the fly; if it's a single-wall tent, it can't be divvied up. However, if you each want a shelter, you might consider adding a 6x8 or 8x10 silnylon tarp (with cord and stakes) to your kit. One of you carries the tent, the other carries the tarp (and tent groundcloth, if you take one), and you each have shelter. The tarp may seem like excess weight just to allay some "silly" fears, but it can serve as a nice shelter to cook in or just hang out in if it rains - especially if you're using a minimal-space two person tent.

I've never used a bear canister, so I can't address you question with any authority. I do wonder, though: do they come in different sizes? If so, would it make any sense to use two smaller ones than one large one, so you could divide the food?

Of course, these types of re-distribution mean that your wife will pay the price of carrying a heavier pack than your distribution would give her. It's up to her to decide how much extra weight she's willing to carry to achieve peace of mind. Respect her decision on the matter - and realize that it might change after a few miles on the trail, at which point you can take back some of the weight.