Long form is way better online these days. I'm working in this field, and I'd expand on your reasons greatly:

• Long form journalism doesn't sell papers -- the sports pages do. As advertising dollars erode, this kind of journalism WILL go to other venues, be it regional or highly local papers or the web.
• The audience for long-form investigative journalism is almost certainly mainly well educated and mainly online.
• The physical constraints of the format and the distribution mechanism of newspapers means is outdated: You can create much richer context around a story -- using multimedia, 3rd party resources, etc -- using good old hyperlinks.
• Layout and design still matters -- you still have to produce online pieces. But it doesn't require a genius to do this -- certainly not the many layers of bureaucracy I hear about from reporters at the Post and the Chicago Tribune in getting their work online.
• If you want a printable version (perhaps of a culmative project), provide it as a PDF.
• Online resources are far easier to track, note, and share with tools like Google Reader or Zotero.
• The Internet is at least as great a venue of influence as printed material these days -- big, big stories have debuted online in recent years. If part of the point of long-form journalism is to influence discourse, policy, and decision-making, then you need to go where you have leverage.

• That quote -- 'If you're doing long form, you should do it in print' -- is pure, unadulterated dogma, unmoored from any reality. If you're doing long form, you aren't doing it for the dailies or the alternative weeklies anymore, most likely. Some, if not all, of your professional life will be online or bump up against Internet technologies. If you need a printed product, you have options (get your audience to help; print high quality single page magazine-covers-without-the-magazine with story snippets and your URL...), you can do events, but your primary channel of distribution is very likely going to be the Internet.

  People who are whining that a story whose primary audience is probably 99% online didn't make it into a format that is hemhoraging money are out of their damn minds, and probably will soon be out of business, too.