Here, the Scarecrow makes an economic decision as to how to cause the most destruction in Gotham City. He makes the classic villain mistake of waiting to execute his master plan in hopes of maximizing pandemonium.
It can be argued that, figuring the Batman is indisposed, Scarecrow assumes the costs of waiting are low. But surely the Professor must have considered that Nightwing, Robin, Spoiler, Batgirl, Huntress, etc. might have arrived to stop him. Besides, he could not have missed the fact that there are some crazy Batman impersonators running--one of which having a robotic suit, wielding guns, and exercising a much more harsh brand of justice than the original Batman.
If I were Scarecrow, I would have gone ahead and pushed the button. Too many villains have their plots foiled by mistakely underestimating the costs of waiting. Besides, I wonder if infecting only a portion of Gotham's population and having those people attack the rest of the uninfected in a mad panic would have been more satisfying. He might have been able to achieve a similar wave of fear and saved some gas for future use.