I think it would be a brilliant addition, if examine mark and other rogue perks could cross over to the Assassin class. I spoke to a DM a while back about this and he mentioned it might just be an oversight. If it's not, then I think it is good food for thought.
As I understand rogue perks doesn't go away when multiclass with PrC.
I think he means progression, not just "you are no longer pure and thus loose certain bonuses) but actually gaining further feats - or, if you dont have access to the Examine mark skill already (i.e a non rogue assassin) you gain it
First, I think is very much an EIG thing, second, I can see it. and I agree personally.