You're essentially asking for automatic upgrades in intra-site modules. Unfortunately, the way modules are upgraded is by comparing assembly versions. Since intra-site modules don't have their own assemblies, this functionality is not supported there. You'll have to manually execute the needed changes in the model when you change your module files.
For more information about upgrades in regular custom modules, you can read this blog post: http://www.sitefinity.com/blogs/slavoingilizov/posts/12-06-28/versioning_and_upgrades_in_custom_modules.aspx
As a workaround, you can implement custom code in the application's global.asax file which checks the state of the database when the application is started and compares is to the required one in your custom module. However, we have not tested such scenarios and recommend you implement a module in its own assembly.