You should be able to output a pickup from a semi-acoustic or acoustic/electric without issue. Your pickup should output the same type of signal as an electric guitar would (or iRig 2 also accepts line level signal). I would recommend opening a ticket with IK Support if you have not already done so. You can do so at
http://www.ikmultimedia.com/contact-support where you are presented with FAQ and can search FAQ and if you don't find a solution within the FAQ the option to open a ticket will be available to directly contact them. Thank you.