For starters, your guidance counselor is wrong. (Not the first time “The Dean” has said THOSE words!) Most engineering colleges require a recommendation from one math OR science teacher, although your daughter may encounter some programs that require one from a math teacher specifically. However, before she proceeds, she should read the application instructions for all of her target colleges (which can be something of a treasure hunt) to see exactly what is expected. She may find that a math teacher’s rec is not necessary at any of her target schools.
If she does find that a math recommendation is required, she can send it in as a supplementary one and still use the physics and econ teachers as her primary supporters. (In other words, she can send three recs instead of two.) In the “Additional Information” section of her application (or in a letter) she can explain that her math teacher barely knows her which is why she’s sent the extra. Keep in mind, however, that if your daughter will continue to take math next year as a senior, she may have a newteacher who will get to know her by the time that her applications are due. She may even have a teacher for a second time who taught her previously (e.g., freshman year) and who could get to know her better by the college deadlines
But, on another note, even for engineering majors, some of the elite colleges like to see references from junior or senior teachers in “core” subjects that include both the math/science and humanities fields. So, instead of the econ teacher, is there a junior or senior English or history teacher who might be able to tout your daughter’s strengths? If so, I’d suggest using this teacher (plus the physics teacher) rather than econ. But if your daughter feels that her econ teacher is really the top choice, and she can’t think of an English or history teacher who would be up to the task, that should be fine. Going with econ won’t be a deal-breaker. In any case, the lack of a math teacher with the inside scoop on your daughter may end up being a non-issue entirely.