I believe that I had read in the basic guidelines a while back that we were not supposed to include periods, such as in the case of. J.M. Williams. However, I cannot find this ruling anymore.
Including punctuation is completely up to you. Some Field Helps (purple question mark), state the following:
In web indexing, you can include punctuation when typing information; however, punctuation is not required.
It is important to check the field helps for every project as all instructions are not the same. There are projects where the field help WILL tell you to include all punctuation. The most recent time that I recall where we were told to include all punctuation was in the Virginia Marriage project.