It is important to realize before we get started that this error was also present within SharePoint 2007. When creating timer jobs, it is important to understand the relationships between the SPSecurity.RunWithElevatedPrivileges method and the associated SPWebApplication object. When using SPSecurity.RunWithElevatedPrivileges, it will not allow modification of the SPWebApplication since it is persisted to the configuration database. However, other proxy objects are exempt from this such as SPSite ‘s and SPWeb ‘s. SPSecurity.RunWithElevatedPrivileges allows the elevation to just the content database, NOT the configuration database (which has the SPWebApplication property bag) which is generally more locked down.
The easiest way to fix this is to impersonate the user account for proxy objects (assuming you are using a current context to reference the application property) with an account that has the wss_content_application_pools database role for the config database since this will have elevated rights for stored procedures and what not. This will allow you to modify your timer jobs easily. If you want to be really lazy, just use the same account as the central admin app pool which inherently provides the required access to the configuration database.