You can add a valve to the intake piping to open if the vacuum goes above a certain value (say vac over 22InHg). OR they make cylindrical filters with a clamp on both ends which you can add to the pipe further down... they're small enough that little air will be pulled in through them as long as the primary filter isn't clogged or submerged (AEM makes one).
EDIT:
http://www.aemintakes.com/air_bypass_valve.htm