It shouldn’t be a problem, although I don’t really think that the Typhoon symbolises anything like a plague. Scurrying rats might be better but I don’t think anyone has created such an animation.
Anyway, just copy Typhoon_Attack.flc to:
CivIII or CivComplete\Conquests\Art\Animations\Plague folder. Rename the existing ‘plague.flc’ as ‘plague original.flc’ and then rename the copied ‘Typhoon_Attack.flc’ as ‘plague.flc’.
That will retain the original in case you wish to return.
There is one thing though – the plague.flc is a single camera SW perspective, slow speed and surrounds the city icon. The Typhoon_Attack.flc is an eight direction perspective, fast speed and should cover the city icon.
Nevertheless, the typhoon animation should work just the same as the original plague animation when the city succumbs to that fearful disease.
Let me know how it turns out.