You can use the hibernate.revenge.xml (it may be called seam-gen.revenge.xml) or something to prevent these columns from being generated. You have to do this for every table however, which is a pain.
You then have to copy and paste the actual mappings into each class, there is an annotation that tells hibernate the database generates these values, I think it is something like @GeneratedValue.
The way I would do it is to get hold of the templates that seam-gen uses to generate the entities. These used to be in the hibernate tools source, but I am not sure where they are now (I have not looked at seam gen since the 1.0 days, so I am not sure how much it has changed). You can then make changes to these templates and tell the seam-gen buildfile where to find your new improved templates that automatically map these columns correctly.
If you want to go down this route but are having trouble I can give you step by step instructions if you need it.