If i understand this: someone who is too easy to raid will quickly be worth next to nothing, so instead of raising white flags or defending their compounds, many might try to give away their flags to whoever comes first?
Here are some possible suggestions for solutions:
1. Check number of attackers and defenders, and: (defender losing points)
1.a: if there are many defenders and 1 or 2 att., and raid is not successful - it should improve defender's rating, but only slightly.
1.b: in same case, but with flag captured, defender should lose war points from his score and alliance score for giving away his flag too easily, and especially if none of defenders were downed, and none of the cades and stuff were broken in process -- or in other words: no effort was made to defend the flag.
1.c: defenders who leave their base without protection too often should also lose points when giving easy points to raiders from other alliances. (applies to 2 or less defenders in base)
1.d: if attacker can simply walk through defender's pound unhindered, take some more points from defender (ie: attacker entered at one side of map, went into barracks, and left map on opposite side) and give them to attacker
2. Check effort made to defend and if reasonable effort was made to defend: (give some points to defender)
2.a: successful defence should give defender... say 50% of points that attacker would score if raid was successful?
2.b: to avoid lame and half hearted raid attempts make longer return times after raids in which attacker pulled out without having any attackers downed by defence and strip them of the number of points that are given to defender.
2.c: successful defence if there are 2-3 defenders and 4-5 attackers should bring even more points to defender.
3. Additionally motivate attacker: (extra points for secondary tasks)
3.1: Walking all over the place as explained above should take some points from defender and give to attacker.
3.2: If possible trough engine, observe where the best equipped defender is (gun with biggest DPS), and make nearest cade or storage next to him a secondary target for attacker. That way if attacker can get to that point and destroy it or loot it, he gets extra points, and you ensure that he is motivated not only to take give-away flags that are placed near the deployment zone (which would not be worth much), but also to into the thick of the battle to get more points.
So these are some ideas thrown in at random, but think about them. ;0)