The species where warp-capable but the war has destroyed all of that technology a very long time ago.
This sentence, all by itself, basically throws the Prime Directive out the nearest window.
If this is a star fairing species, even if they have no warp drive "at the moment," then one of the biggest reasons the PD exist, to protect primative species from the certain knowledge that intersellar life exists, is void.
Also, this star fairing species (one faction) has taken a Starfleet captain prisoner, maybe even hostage, after shooting down a federation shuttlecraft. That's an openly hostile act against the united federation of planets. Possibly even an act of war.
Their technology, and their knowledge, can't have fallen to far if they can still shoot down a 23rd/24th century Starfleet shuttlecraft.
The Commander is now on much firmer legal grounds for her actions.