I hear you. I think most LHBS owners feel the same way you do since they seem pretty opposed to facilitating bulk buys, because they fear the lost profit from those grain sales.
If I were an LHBS owner, I would want to move as much grain and other supplies as possible through my store. Brewers who buy bulk base grains also buy a lot other stuff, like specialty grains, hops, yeast, equipment, books, etc. As an LHBS owner, I would want these heavy users to come to my store first. So, I would be willing to give up the profits on a some of my base grain sales to build good will among this core set of customers.
Good will and customer service can go a long way to building a successful business. If facilitating bulk grain buys for heavy consumers of other brewing goods would help build a good reputation for my store, then I think I would do it.