During an application/interview should an applicant justify leaving a current faculty position (pre-tenure)?

It's not uncommon for people to move because of two-body issues, and if you're not comfortable disclosing the specific reasons, one possibility is to mention (at interview time) that you have non-academic constraints that force your departure from a place that you like.

Having said that, you're not going to get an interview call unless you're a superstar and everyone wants you OR you have some positive argument for why you're interested in a particular university. So in your cover letter you'll at least need to provide some positive reasons.