I don't see any reason why Capybara's can't be in walkthroughs. Though I can't recall any Capy walkthroughs at the moment, I'm absolutely certain there are some
There are some in Japan at least - I'm not aware of any in NA, not sure on Europe. Generally worth bearing in mind that while Capys are generally easy going, they are still sizable animals with large teeth.
would a walkthrough of Patagonian mara, Greater rhea, Chilean pudu and (possibly) guanaco work?
*if the guanaco makes this not walkthrough safe then i can remove it.
Probably fine, though I'd probably at minimum prohibit the guanacos from having full access to the guests or keep them away entirely. You'd want to choose your rheas carefully too if they're allowed to walk among guests. The pudu might be a bit reclusive in this situation as well.