Can I set a theme's logo_path programmatically?
In Drupal 6, I believe what you are looking for is

variable_set('logo_path', '/path');


At first glance though, I'm wondering why there is only one such on my site, and not one per theme.
theme_get_settings appears to be grabbing defaults first, and then merging in theme specific settings on top of that.

In D7, the variable is called 'theme_themename_settings'.