As someone kinda obsessed with handcrafting all of its software without any dependency and is highly used to dom operations, I can't but thing you're making it much more of a deal than it is.

Handcrafting JavaScript applications without jQuery is possible, the real question though is: is it convenient if you like and find productive using jQuery? Here's a fact: you can always remove jQuery later when the product is mature and standards understood and there is time budget for it.