Had a flat this weekend and Hertz offered reimbursement for the repair up to $25. Since I was home in SFO, I just drove the mile to return the car on Mason St. rather than deal with the repair and had no problems with the exchange.
I tend to think that Hertz would reimburse you for any reasonable tire repair expenses. Why don't you call Roadside Assistance again?
I wouldn't expect more than a new car if you decide to exchange the vehicle.