You could edit the inner cortical mask.
Just before you press generate inner cortical surface, goto tools->mask tool
There I assume that the ventricle would be empty in the mask. You can edit it and fill the ventricles.
Then generate the inner cortical surface and continue.
This should take care of the issue.
You can also manually edit the final labels manually using the label tool.
In case of abnormal anatomy, the results would depend on the extent of the abnormality. In general, the unaffected hemisphere should still be fine.