School prayer has been a hotly contested issue, especially in Texas.  However, if your Little League organization is a private organization, then the group of private people can decide to have a prayer and hold meetings where ever they are able to hold a meeting, inlcuding a church.  You have a couple of options if you don't agree with the organizations decisions.  First, many little leagues have boards that set the rules, so you may want to become a board member so that you can have more direct input.  A second option is to look for a different program that does not involve prayer.