Actually most big alliances solved this problem by not letting in smaller prestige players (600k or less) because they can not contribute resources or troops to the alliance.

I have had resource trades intercepted when my transport went through to them, their's to me was intercepted, and they were players with 4-500k prestige

There are ways around these limits, but its not worth the hassle, easier to just kick them. They must then join small alliances which can be easily farmed by the bigger ones.