Wars are not fought over alignment per se.

Real life examples: crusades, World Wars, Gulf War etc.

Do you believe that in each of these wars one side was evil? No. There are "lightwalkers" on both sides fighting because they have different beliefs, values, information etc.

The sylvan warlock one is analagous to this to the extent that, although the warlocks are all lightwalkers, they are fighting over a point of principle, as are the sylvans.

The same is true of the village vs warlocks. Both the sylvans and the village include lightwalkers, but they both have reasons to fight the warlocks that are not linked to "evil" except in individual circumstances.