If you load the mat file into a struct (i.e. the load option with output argument), then your variables become fields of that struct which allows you to rename them (renaming variables themselves is not a fun task). You can then save the struct back out to the mat file with the '-struct' flag.
e.g.
varStruct = load( matFile );
...
save( matFile, '-struct', 'varStruct' );
As far as code goes to actually do the structure field renaming though I don't have time personally to do that, but someone else probably will and it should be simple string manipulation with functions such as strrep.
Bear in mind you can access a field name of a struct using a dynamic string as:
myFieldName = getFieldNameStringFromSomewhere();
myStruct.( myFieldName );
rather than having to hard-code the fieldname.
