I don’t think you caused a chillul Hashem with your explanation.
I’m confused about how the situation came about. If there was a card and envelope on someone’s desk, why couldn’t you just sign the card with your sympathies and put nothing into the envelope? If the envelope was stuffed with a mixture of cash and checks, how could the administrative assistant keep track of who donated or not?
Personally, I feel uncomfortable with the idea of someone going around collecting donations at the office, especially if it’s a manager or someone close to a manager. I think that it was downright inappropriate for the administrative assistant to ask you why you refused to donate. The problem wasn’t with your response, but the fact that you were asked the question.