Will a graduate student publishing in different disciplines confuse potential employers?
The only real danger you will have with prospective employers (presuming that you look for a postdoc before your faculty search) is that a potential advisor might be concerned that if you aren't engrossed in their research, you will seek out opportunities in other areas. If it's their money that's supporting your time, then you'd be expected to devote your effort to the line of research you've been hired to do, not what you'd like to do.

This is something that you'd have to explain in your cover letter in any case. But you'll need to explain—as you have—that your lateral move was encouraged and done with the support of your current advisor. Otherwise, it could be a concern.