If anyone deserved to use a flag on a logo saying HERO it’s this gal.
Just consider it my way of taking it back. Like how some people have started to take back the rainbow symbol from the (usually not gay) homosexuals.
Your rationale makes some sense — but, it requires the engagement of the left brain & the verbal explanation you've just provided. Interpretation of graphic messages is decidedly a right-brain function & occurs almost instantly. The graphics (unfortunately) imply Obama is a hero.
The other Obama dollars I've seen link Obama & his logo to negative qualities or events. In this case, you've (obviously inadvertently) linked Obama (through the logo) to something positive (heroism).