Super late to the party. The only flaw I can see in the proposal is that there really is a balance problem with individual attackers going after their enemy alliance's members IF the member they go after is significantly LESS in power than they are. Because they get the bp boost no matter who they attack on the enemy's side, the lower-point players will be descended upon like bait for easy points, quickly driving them off the server, or out of the game if they're new. This could also potentially create a culture of new players being discouraged from joining an alliance out of fear of becoming easy targets with benefits which would cause a loss of community/group learning that would otherwise come from joining an alliance after getting the hang of things, or some more seedier alliances to suddenly begin sending out invites to one-city players to use as fodder against enemies in war, etc. The amount of bp gained with the boost should be directly proportional to relative size of the enemy being attacked- if they're half your size, maybe you only get 1/3 of the total possible points. If they're on par with you, then you get 100%. If they are above your point level and you beat them, you get 110%, or something of that nature. Incentive should be to look for worthy opponents to battle, not players who are newly in the throes of expansion with only one, two, or three cities to their name. So, I feel that there's potential abuse with that one hole.
Otherwise I do think it's a good idea. Unfortunately I'm contributing way too late for this issue to count now. Because of that, I'm abstaining from voting yea or nay on this development in the poll.
EDIT: After looking over some of the finer points on previous pages more carefully, my suggestion here would satisfy the concerns of thefbiman and others who were worried about similar issues albeit for different reasons. If reward bonuses, or even rewards, in war mode depended more on your point value versus their point value, it would help even the playing field out a bit- new players wouldn't get harassed for being small and on the 'wrong side', and going after ghosts for bp would be almost a waste of time since you'd get very little, if anything, for it. Instead of making it an alliance score vs. alliance score, making it player score vs. player score would tailor the fighting better to appropriate matches. This could also encourage alliances to recruit a more varied player base, because the closer and more appropriate the match, the more gains for the alliance. So you wouldn't need an alliance full of 20k+ players to more quickly further the alliance- if you're in war and your enemy has a 4k player and you have a 4k player that attacks that 4k and wins against them, that would gain the alliance and themselves more bp than if a 10k went after them instead. If that makes sense.
Sorry for the essay.