Indeed, for controlling DC motor, a DC motor controller is the best choice, which is a half-bridge (synchronous or non-synchronous) without LC filter. Requirement for current sensing is the same, though.
DC motors provide a lot of inductance for you; so much you would never use such large amount if you designed an equivalent DC/DC supply. But the inductance is there for you: you can as well use it! This large inductance means, f_sw will be significantly lower, and ripple current will be lower as well, than what you would design for a DC/DC power converter. Some 10kHz usually works well from the ripple current viewpoint; you may want to go just beyond audible range, though.
End result will be single-phase, though.
Any PWM generation unit then works for this purpose, no need to use HRTIM especially. It's a plus if the overcurrent comparator signal can be connected to the timer directly, STM32 Advanced Control Timers have such break input that can be routed from the internal analog comparator, but software interrupt can be acceptable too if you do this with a simple 8-bit AVR/PIC for example.