Yes it is. You can intercept something for good or for ill, there's no connotation there, but it does imply some degree of intent to capture something.

These researchers fully intended and expected to capture some e-mails. They didn't want to steal them, they weren't doing anything wrong, they just wanted to see how many e-mails they'd get and write a paper. I'd say intercepting the e-mails is at least a better description than theft.