Doubly-stochastic point processes model the occurrence of events over a spatial domain as an inhomogeneous Poisson process conditioned on the realization of a random intensity function. They are flexible tools for capturing spatial heterogeneity and correlation. However, existing implementations of doubly-stochastic spatial models are computationally demanding, often have limited theoretical guarantee, and/or rely on restrictive assumptions. We propose a penalized regression method for estimating covariate effects in doubly-stochastic point processes that is computationally efficient and does not require a parametric form or stationarity of the underlying intensity. Our approach is based on an approximate (discrete and deterministic) formulation of the true (continuous and stochastic) intensity function. We show that consistency and asymptotic normality of the covariate effect estimates can be achieved despite the model misspecification, and develop a covariance estimator that leads to a valid, albeit conservative, statistical inference procedure. A simulation study shows the validity of our approach under less restrictive assumptions on the data generating mechanism, and an application to Seattle crime data demonstrates better prediction accuracy compared with existing alternatives.