No, choices in side quests can effect that specific series of quests (if there are several related) and relevant NPCs, but not the main plot quests.
In this case, I helped Richard my first game (he isn't asking for help ferrying food to Aleroth, but stealing food destined for Rivertown), and sided with the New Order my second. Refusing Richard's request can lead to a better reward, though should probably be delayed until you have cleared Broken Valley and exhausted the supply of goblin hearts, as after that quest path, Richard will no longer be in the village.
If you refuse to help Richard, he heads to the farm himself to commandeer the food. When you arrive you can choose who to help, and fight the opposite group; if you side with the New Order and kill Richard, you can Mindread Lomax for a stat point in the automatic dialogue after the fight.
