Bring a large pot of well-salted water to a boil for the pasta.
Heat the olive oil in a large non-stick skillet over medium heat, add the crushed garlic and crushed red pepper flakes, and cook until the garlic is fragrant and just beginning to brown, about 3 minutes.
Add the canned whole peeled tomatoes (roughly chopped) to the skillet, break them up with a spoon, and simmer over medium-low heat for about 10 minutes.
Add the fresh cherry tomatoes to the skillet and simmer for an additional 10 minutes, until the sauce has slightly thickened.
Stir in the canned cannellini beans and return the sauce to a gentle simmer; season with sea salt to taste and keep warm over low heat.
Cook the whole grain penne in the boiling water according to package instructions until al dente, being careful not to overcook.
Drain the pasta and transfer it to a large bowl.
Add the hot tomato-and-bean sauce and the baby arugula to the pasta, then toss with a large spoon until the arugula wilts and everything is well combined.
Divide the pasta among warm bowls and top with grated Parmesan if desired.