Sharepoint 2007 : How to set column level permission

I would use jQuery for this purpose. Here is an example that describes how to hide a text field on a SharePoint form. Change the .hide() to .attr('disabled','disabled') and this will disable the text field.

If you need help with deploying jQuery, see this question.

You are correct that it's not possible to set field-level permissions without custom code. Furthermore, you're on the right track thinking separate lists, though you should be aware that SharePoint list lookups are a rather weak correlation. Usable, but not exceedingly robust.

For presenting the combined data you'll want to look at SharePoint Designer's joined subviews.