That's not possible at the moment. Namespace separation has been requested a couple of times, but it wasn't really solvable. The thing is that the code generated is more than just the entity classes. So if you divide up the set of entities in groups, the code generated for these classes also has to be split up into groups, e.g. relation classes, collection classes (if you're using selfservicing), factories etc.
This effectively comes down to generating code per group in a separate project which has the downside of not having the relations between the groups.
So the code in the templates has to be re-organized to support this, and currently that's not possible: it has to have a group of 'shared code' and then for each group the code for that group in a separate namespace. Though if two entities A and B have a relation and A is in namespace X and B is in namespace Y, the relation A-B is in namespace X and the relation B-A is in namespace Y. This can be cumbersome, both in usage and in the underlying code.