I'm a big fan of the Euler typeface for mathematical typesetting, especially compared with the standard Latin Modern. I feel somewhat justified in changing to Euler for a paper, but Euler doesn't usually look very good with the default body text typeface.
It's a small thing to change that as well (\usepackage{charter}, for instance), but at that point you're really messing with the official style supplied by the conference.
On the other hand, some conferences also allow submissions from Word documents, so the visual unity is unlikely to be maintained anyway.
So, two questions:
- How unusual and frowned-upon is it to change the math typeface?
- How unusual and frowned-upon is it to also change the body text typeface?