iTunes will automatically convert video and songs into formats supported by iPods.
You can use ImTOO MPEG Encoder to convert the video you want on iPod to ipod mp4 format. And then use ImTOO iPod Computer Transfer to import the converted video directly to your iPod without iTunes. After that, you can deleted the converted result video and just keep the original one on your computer.
You can free download ImTOO MPEG Encoder at
http://www.imtoo.com/mpeg-encoder.html
and ImTOO iPod Computer Transfer at
http://www.imtoo.com/ipod-computer-transfer.ht ml