How about a warning, "Flash will eat your battery"?
It seems reasonable to let the consumer make the decision if Flash is that important that they will let Flash load or not.
When I go overseas, I turn off data roaming so I don't lose my shirt to data charges when I come back. Every time I need to use data (maps, stock, weather, mail, etc) I get prompted that I need to turn on data roaming. After I am done, I turn it off again, so that mail doesn't keep grabbing mail and the overseas carrier charges me per KB.
Same should go for Flash. By default a flash player should be turned off. When you enter a page that requires flash, a warning should come up asking "Would you like to turn on flash for the page you are entering? Use of Flash may dramatically reduce your battery performance."
You choose yes or no (you're a big kid now).
Meanwhile, the iPhone could display a flashing battery icon reminding you that you are in a high consumptive mode.
As soon as you move out of the page (or minimize safari) the flash player stops (and battery consumption drops to normal).
If you move to a second flash page, the same message comes up, this way you don't leave the iPhone in a high energry burn state. Maybe acknowledging these per-page warnings would be a nuisance, but I would prefer to only activate Flash when needed, and not be shut out of Flash-only web sites.
I'm not a programmer, so it sounds like a simple solution.