It seems to me there is a common phrase that applies here, something about a soft word turning away wrath? Specifically, you might want to mention to your secretary that you enjoy the scents she wears, but their strength is a little overpowering for you. You could then ask her to try to use less perfume and see if that helps. This way you aren't expressing a negative judgment about her fragrance quality; you're just asking for an adjustment in quantity.

If you still can't stand being around her, you might need to ask her to stop wearing perfume altogether. There isn't anything picky or silly about asking her to make a concession so you are able to work with her without holding your breath. Maybe she just isn't good at judging how much scent she puts on, or maybe it is that particular fragrances are harder for you to tolerate, but your comfort at work is certainly at least as important as her freedom to wear perfume!