How about this?

You were probably trying to reassure her that it was not a big issue, and, in using the word "ignore" you meant it in the sense that, given her obvious value to the company, her commitment, and level of achievement, that it was a minor issue, and you intended to convey that it was not necessary for her to overreact, rather than to literally suggest that she "ignore" her boss.

I worked for the government, then in public relations and advertising, so I have had to weasel out of many unfortunate word choices--well, not "weasel", lets say "constructively reinterpret"--