With Pentadactyl, what you describe just isn't a problem: the extension captures the keys and prevents websites from screwing that up, unless you want to access them, in which case you just press C-z to enable 'Pass Through' mode.
I realize it's not fair to expect web app developers to adapt to my (or anyone else's) custom browser configuration, but in this particular case, they're adding vim hotkeys primarily as a convenience to fellow vim users, not as a defining feature of their site. Given that, I think they should be aware that there is a subset of those vim users who are negatively affected by their kindness.
Humorously, Chrome just completely crashed while I was writing this (running on the latest Quantal beta), prompting me to remove a bit I wrote about Chrome being more stable than Firefox due to its process isolation. I have a hunch that the fault lied in the Flash plugin, however, which doesn't seem to be terribly stable on Linux. I've never had a browser-wide crash on Chromium in the past, but not being able to watch certain Youtube videos and missing the convenience of Chrome's PDF plugin prompted me switch to it. Not sure I made the right decision.