After reading up on this as much as I can, here's what seems to have happened.
The central point seems to be that the local Council was being asked to have their leaders take training on how to deal with issues of youth and sexual identity. Apparently this training was to not only include trying to understand the issues and emotions that a young man who was confused about his sexual identity would be feeling, but also to teach the leaders to refer such a young man to organizations outside of his own family and religion.
The former is acceptable. You need to understand young people's emotions and developmental stages to be able to work with them effectively. However, the latter is unacceptable, as the purpose of the BSA is to support and supplement a Scout's family and religious community, not to provide an alternative to them. BSA leaders will only refer a Scout elsewhere in cases of abuse, and then only to the proper authorities.
Now, it may be that the local Council may have agreed in principle for "sensitivity training" for their leaders without getting a detailed agreement on what that training's curriculum was to be. That was an error, which they should admit.
It may be that there was a proper agreement, but that the local gay advocacy groups tried to change the rules after the agreement was signed. That should be made public, if true.
Finally, it may be thatt the local Council was willing to do what was being asked, but that National Council found out the details and (properly) overrode them. If this is the actual case, I doubt that National will make this public. But, if the local Scout Executive is replaced soon, I'll come to figure that this is the most likely scenario.