I don't breed, so I don't have any first hand experience with this, but in the wild, does only go to feed their kits once a day. They spend less than 5 mn a day with them to avoid predators following them and finding the nest, mostly (which is why I'm always baffled by people who tell you that does need to have kits to feel 'fulfilled'... they barely see their youngs and certainly don't have much of a relationship with them). It's also why a lot of pregnancies goes badly in captivity - some people lock their doe in a small cage with the kits which leaves her no escape from them and can stress her out. As long as the kits are fed at some point, I would leave the doe free to get away from the kits when she doesn't feel like putting on with them.
And yes, the alfafa is probably responsible of the urine's color.