A site must be always visible in Google by it's name. Especially it's very important for huge sites. In most cases people search for these exact sites when they use such queries.
Why people use Google to enter to an exact site? It can happen for many reasons:
1) A surfer uses a search bar of his browser instead of an address bar.
2) A surfer uses an address bar, but he only remembers a third level domain name. For example he types "domain" instead of "domain.com
" in an address bar.
3) A surfer doesn't remember an exact address of a site. But he remember's a name of a site. He uses address bar, search bar or does a search via google for a site name.
4) A surfer uses Google to find internal pages on an exact site.
5) A surfer has Google as a default page of his browser and uses it's search bar instead of an address bar of a browser.
Probably this list is not complete. But it shows that almost each site on the internet has a group of people who enter this site using it's name.
What happens if surfer can't find a site which he searches for? In most cases he is getting unhappy. Some of these surfers stop using Google to enter to their favorite site. They use an address bar instead. But those who only know how to find this site via Google have no choice. They are loosing their favorite site for a very long time.
That's why I think that even if Google penalizes sites they must be always visible by it's own names. Making them invisible will simply decrease a quality of a search.
Of cource this is only my personal opinion.