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We propose an architecture for achieving high-fidelity deterministic quantum logic gates on dual-rail encoded photonic qubits by letting photons interact with a two-level emitter (TLE) inside an optical cavity. The photon wave packets that define the qubit are preserved after the interaction due to a quantum control process that actively loads and unloads the photons from the cavity and dynamically alters their effective coupling to the TLE. The controls rely on nonlinear wave mixing between cavity modes enhanced by strong externally modulated electromagnetic fields or on AC Stark shifts of the TLE transition energy. We numerically investigate the effect of imperfections in terms of loss and dephasing of the TLE as well as control field miscalibration. Our results suggest that III-V quantum dots in GaAs membranes is a promising platform for photonic quantum information processing.