Heat a large pot over medium-high heat. Pour in oil, then add onion, carrots, garlic, 1 tsp. salt, the red pepper flakes, and bay leaves. Cook, stirring occasionally, until vegetables have softened and onion is translucent, 6 to 8 minutes. "It's important to cook your onions before you add liquid. Otherwise they won't melt in a simmering pot; they stay fibrous," advises Smith.
Add tomatoes, crushing them up with your hands, plus their juice and 2 cans water. "Canned whole tomatoes are usually higher quality than chopped," Conley says. "But chopped are okay in a pinch." Bring soup to a simmer and add half of oregano. Decrease heat to very low and simmer, partly covered, 2 hours. About 20 minutes before soup is done, add remaining 1/2 tsp. salt and the remaining oregano.
Remove bay leaves and blend soup until smooth. Add a bit of water if the soup looks thick, and strain if you want it silky smooth.
Serve soup topped with crème fraîche and chives.