Don't be dissuaded so easily - Heifer is a great organization.
They have a campus (learning center, business office, and functioning farm) in Rutland, MA, which is just one town away from me. I've been there many times. The folks who run it are great people, they attract lots of young volunteers, and maintain excellent missionary programs in numerous developing countries. They also give back to the local community, with events at the farm, summer camps, and educational programs at local schools and churches - yes, of course they're always looking for donations at these functions (as they should), but it's a happy quid pro quo. They bring livestock in to our church for the living Pageant at Christmas time - it's so funny to see a donkey walking up to the altar! :-)
We donate every year. We usually donate in other people's names, as Christmas gifts, etc. After all, what kind of holiday gift do you get Dear Aunt Tillie, or the neighbors you hardly ever see? You can buy a bee hive, or some baby chicks, or a share of a cow or something in their name - Heifer gives you a card explaining what the gift is. Aunt Tillie will love it, you'll feel good about it, and the money will go to good use.
As for whether your money goes to individual gifts or the general fund, they are very up front about this. I think it's just impractical to manage every single bunny, chicken, or bee.