I know this is a rather old post, but I am also running alias problems with my setup. For me (version 8.0), I cannot create aliases on any field if the data source is a data source or extract published to Tableau Server. This is pretty frustrating, and I have not been able to find a reason or a fix.
Here's the workaround though - and should work for you as well: If you need an analysis, duplicate the field first. You can set an alias on any NEW field created on top of the extract/saved data source. When you publish, you should lose your alias.
Again, very frustrating but it works.