Regarding lines 171 to 178:
* For panels and other modules that may set $show_blocks to false, we will need to
* unset the sidebars in this case
if (!$vars['show_blocks']) {

For Views 6.x-3.0+71-dev, which is the current packaged dev version of Views 3 for D6, these lines generate the following undefined index errors:

notice: Undefined index: sidebar_first in /var/www/sites/all/themes/omega/template.php on line 163.
notice: Undefined index: sidebar_last in /var/www/sites/all/themes/omega/template.php on line 163.
notice: Undefined variable: sidebar_first in /var/www/sites/all/themes/mytheme-omega/page.tpl.php on line 132.
notice: Undefined variable: sidebar_last in /var/www/sites/all/themes/mytheme-omega/page.tpl.php on line 138.

Apparently Views is being smart about the sidebars, and commenting out these lines has worked for me. It hasn't lead to any other bugs that I've found yet, but of course I may be speaking too soon.

I'm not using Panels, so haven't found any interactions there. I'm not sure what the solution is: if Panels requires this, but Views 3 wants the sidebars set, then ...? Otherwise I would have suggested a test for whether Views 3 was running. Perhaps the solution is to change Views back to what must have been prior behaviour.