We consider the problem of safely coordinating ensembles of identical autonomous agents to conduct complex missions with conflicting safety requirements and under noisy control inputs. Using non-smooth control barrier functions (CBFs) and stochastic model-predictive control as springboards and by adopting an extrinsic approach where the ensemble is treated as a unified dynamic entity, we devise a method to synthesize safety-aware control inputs for uncertain collectives, drawing upon recent developments in Boolean CBF composition and extensions of CBFs to stochastic systems. Specifically, we approximate the combined CBF by a smooth function and solve a stochastic optimization problem, with agent-level forcing terms restricted to the resulting affine subspace of safe control inputs. For the smoothing step, we employ a polynomial approximation scheme, providing evidence for its advantage in generating more conservative yet sufficiently-filtered control signals than the smoother but more aggressive equivalents realized via an approximation technique based on the log-sum-exp function. To further demonstrate the utility of the proposed method, we present bounds for the expected value of the CBF approximation error, along with results from simulations of a single-integrator collective under velocity perturbations, comparing these results with those obtained using a naive state-feedback controller lacking safety filters.