© 2019 authors. Published by the American Physical Society. Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI. Similarity transformation of the Hubbard Hamiltonian using a Gutzwiller correlator leads to a non-Hermitian effective Hamiltonian, which can be expressed exactly in momentum-space representation and contains three-body interactions. We apply this methodology to study the two-dimensional Hubbard model with repulsive interactions near half filling in the intermediate interaction strength regime (U/t=4). We show that at optimal or near optimal strength of the Gutzwiller correlator, the similarity-transformed Hamiltonian has extremely compact right eigenvectors, which can be sampled to high accuracy using the full configuration interaction quantum Monte Carlo (FCIQMC) method and its initiator approximation. Near-optimal correlators can be obtained using a simple projective equation, thus obviating the need for a numerical optimization of the correlator. The FCIQMC method, as a projective technique, is well suited for such non-Hermitian problems, and its stochastic nature can handle the three-body interactions exactly without undue increase in computational cost. The highly compact nature of the right eigenvectors means that the initiator approximation in FCIQMC is not severe and that large lattices can be simulated, well beyond the reach of the method applied to the original Hubbard Hamiltonian. Results are provided in lattice sizes up to 50 sites and compared to auxiliary-field QMC. New benchmark results are provided in the off-half-filling regime, with no severe sign problem being encountered. In addition, we show that methodology can be used to calculate excited states of the Hubbard model and lay the groundwork for the calculation of observables other than the energy.