I won't reiterate everything I wrote in that other thread, but, briefly, I think a line can be drawn when the practices of a religion result in senseless violence, degradation and destruction. Would you be able to accept a religion that stated quite simply that your family had to die (either specifically or as part of a class of people)? What about one that said that every second baby that is born, including yours, had to die? I would label that, objectively speaking, as wrong.
On the "hero" question, I would argue that there is a great difference between someone like George Washington, who waged an open, military campaign against a foreign regime, and someone like Bin Laden, who wages a covert war against a foreign nation by destroying even non-military targets. I would venture a guess that Washington didn't run around killing people left and right simply because they were British subjects, nor did he attack non-military targets specifically.
One can look at the legitimacy of the IRA for another example. Had they continued to confine their attacks to police stations or military installations, they would have likely retained more support for their actions. When they decided to start bombing rail stations, shopping malls, and outdoor markets, they significantly diminished their message, at least to me. There is a fairly marked line between a revolutionary and a terrorist.
On the US support during the Afghan war, of course I realize that the reason the US helped the Afghanis was to punish the Soviets and not to help per se. Regardless, without US and British assistance, the Afghanis would NOT have done nearly as well as they did. The Stingers and Blowpipes really hampered the Soviet use of airpower -- if the same capability had been in the hands of the Vietnamese, that war would have ended far sooner. Now, there is no recognition of that fact. Does the US not acknowledge French assistance during the Revolutionary War, which was done not to help the Americans but to punish the Brits?