Position an oven rack in the center of the oven and preheat the oven to 425 degrees F. Spray a heavy baking sheet with vegetable oil cooking spray.
In a medium bowl, toss together the butternut squash, zucchini, bell peppers, kidney beans, oil, cumin, oregano and salt. Spread the mixture in a single layer on the baking sheet. Roast until the vegetables are golden and tender, 25 to 30 minutes.
Split the pita breads in half horizontally to make 4 rounds. Arrange in a single layer on a heavy baking sheet. Bake until crisp, 7 to 8 minutes. Set aside to cool.
In a small bowl, mix together the yogurt, lime juice, agave and chipotle pepper until smooth.
Spoon the vegetable mixture on top of the crispy pitas and serve with a dollop of the chipotle cream.