Hello Sachi, I was referred to your post by a moderator. I am having a similar problem, but didn't realize it from the title of your post.
I have my blog set up as my main website, but I want the home page to be different than the rest of the blog... well in the same framework but have a bit different functionality.
i want the home page to have functionality i specify in home.php but I also want to be able to link to the blog as you would normally see it. like you i am a bit frustrated that there is no link to a page that is the normal index page before i created my custom home page.
your idea of linking to archive/2006 is a good one. I hadn't though of that. the only problem is I will have to manually change thing links come Jan 07, and then my 06 posts wont be easily available to the user.
another solution i thought of was to have one category called posts or something like that and put all my categories in there. that may work.
this really seems like wordpress should have a default URL you can point to like wordpress/all_posts or wordpress_index that will provide the default view even if you have created your own home.php page.