Just an idea:
When you penalize an innerpage you can rename that innerpage, rename the innerlinks pointing to that page and build new links to it. Piece of cake, worked extremely well a couple of times, you can even use the same content cause it's not content that gets penalized but the specific exact url.
As we can't rename the url of the homepage we can do something else as a pre caution before we start building links, so this applies mostly to new sites or sites that you plan to build links to again.
Not sure if this is flawed thinking, I don't think so but here we go. Your very homepage has different types of urls for Google:
homepage.com
homepage.com/index.html
homepage.com/index.php
homepage.com/home.php
homepage.com/home.html
The "internet" treats all these 5 as exactly the same. Obvious the ones with the words behind the / depends on how the file in your public_html is named.
My site is for example homepage.com/index.php , same like the most typical Wordpress site, so what I can do is point all my links to the exact url:
http://homepage.com/index.php , now if I go to wild with my links and my homepage gets penalized I can rename index.php to home.php, and gone are all the bad links pointing at my site, and thus I got rid of my penalty pretty easily (same like renaming an innerpage url helped), while all the rest of the structure remains intact and can help my homepage rank again.
But if you build all links to homepage.com there is nothing to rename.
What you think? Do I miss something here or is it just a genius idea?