Bring a medium saucepan of water to a boil over high heat. Add rye berries and ½ teaspoon of salt. Bring to a boil and then reduce to a simmer. Cook until the rye berries are tender but still toothsome, about 45-50 minutes. Drain the rye berries and set aside.
In a medium saucepan, cook the bacon over medium heat until brown and crisp, about 6 minutes. Transfer the bacon to a paper towel-lined plate, leaving the bacon fat in the pan. Remove and discard all but 1 tablespoon of the bacon fat in the pan. Set the bacon aside.
Add the leeks to the saucepan and cook over medium heat until they begin to soften, about 3 minutes. Add the garlic and thyme and cook for 1 more minute.
Add the white wine and scrape up any brown bits on the bottom of the pan and cook until the wine has nearly evaporated. Return the rye berries to the pot. Add the chicken broth and bay leaf. Bring to a boil and reduce to a simmer. Cook until the mixture has thickened but is still saucy in consistency, about 10 minutes, stirring frequently. Add the peas, cooked bacon and the parmesan and stir to combine. Continue to cook until peas are heated through and cheese has melted, about 2 minutes. Season to taste with salt and pepper. Serve.