I absolutely love Whole Foods, but it does have the nickname "Whole Paycheck" for a reason. I would first check out your local grocery store to see what organic choices they have. Like other posters have said, most grocery stores are starting to provide more "health food" type items so that they can meet the demand and compete with the health food stores. That said, stores like Whole Foods do have some items that you cannot find anywhere else. I purchase a lot of vegetarian items there that I cannot find at a regular grocery store chain. So I would do the bulk of shopping at the local grocery store, then go to Whole Foods for a few specialty items.
If you are looking to go organic but are on a budget, your first priority should be getting all your meats and dairy products organic. Non-organic meats and dairy have the highest concentration of hormones and pesticides as compared to fruits and vegetables. You really don't want your children eating hormone-laden meat and milk. If you can afford it, buy thin-skinned fruits and vegetables like strawberries and tomatoes organic. Unless it's really within your budget, you can skip organic avocados and watermelon since the pesticides generally don't penetrate the skin. Good luck!