For the record, I did exactly what the OP suggests in my first 3E campaign while lowering scribing costs to 1/10 normal. I liked the realism, the players liked the reduced GP cost. Everybody was happy.
The biggest benefit became the fact that certain spells became "special" and rare. Under the rules as written, the only spells that are special and rare are those that are those that PC's or NPC's pay to create from scratch.
I will note that if there were no coresponding benefit and the Wizard only lost the 2 freebies each level, I think it would make Wizards substantially weaker than the other primary spellcasting classes.