Matshopp,
I do not believe that any geoprocessing methods are exposed that will allow a user to permanently change a geodatabase field alias. I'm not sure why, it seems like it would be a very useful geoprocessing tool. Hopefully someone else can tell me that I am incorrect.
For table aliases, you can use the arcpy.AlterAliasName(table, alias) method. I think this is new at 10.0.
In 9.x geodatabases, it was possible (but definitely NOT recommended) to alter aliases by editing the GDB_FieldInfo table. If done incorrectly you could trash the geodatabase so I won't go into further detail.
If you have experience with ArcObjects, you can use the esriGeodatabase.IClassSchemaEdit and AlterFieldAliasName methods. I have used this with ArcGIS 9.3 and MS SQL Server but haven't checked to see if these still apply at 10.x.
-Steve