We just got a new roof two days ago, and now the siding men are using "nail in" type scaffolding to work from... I know he wont change this, so what can be done to repair the "new" holes he's so graciously putting in over and over again?
Unfortunatly this is a common practice here. Siders come in after the roofers and nail 2x4s in the roof to stand on or set scaffolding on. After the job they usually will pull the board and use a mastic to caulk the holes. That works but it is not what you paid for.
IMO you should call your roofer and find out how much he will charge to replace the nailed through shingles. Inform the sider the cost of the repair and that you are going to be withholding that cost from his payment. Since he did the damage he should not have a problem with the solution.
p.s. You should maybe take pictures so you have proof.