Conventional wisdom suggests that single-photon lidar (SPL) should operate in low-light conditions ($<0.05$ photons per laser pulse repetition) to minimize dead-time effects. Many methods have been developed to mitigate these effects in synchronous SPL systems. However, solutions for free-running SPL remain limited despite the advantage of reduced histogram distortion from dead times. To improve the accuracy of free-running SPL, we propose a computationally efficient joint maximum likelihood estimator of the signal flux, the background flux, and the depth using only histograms, along with a complementary regularization framework that incorporates a learned point cloud score model as a prior. Simulations and experiments demonstrate that free-running SPL yields lower estimation errors than its synchronous counterpart under identical conditions, with our regularization further improving accuracy.