Sean Eberhard commented on my posts on diagonal groups (see here and here). He is correct; there is an association scheme preserved by the full diagonal group with n factors in the socle; it is non-trivial if n > 2. The details take a few pages to write out but the basic idea is completely fine.
This shows that an AS-free group (one which does not preserve a non-trivial association scheme) must be either 2-homogeneous or almost simple. Clearly every 2-homogeneous group is AS-free; there are almost simple examples, but they are rather strange and no pattern has emerged thus far.
I hope a preprint will go on the arXiv sometime soon. But you read it first here (in Sean’s comments over the last few days).