Is the scratch on the negative or is it being caused by the scanner? Also, what kind of scanner are we talking about?
It could be that you need to clean the scan bed. Sometimes a particle of dust will get stuck on the calibration area of a flatbed scanner and it will cause an issue that looks like this.
If the scratch is on the negative you could try to target it with iSRD but your mileage may vary.
The easiest way is to fix it in photoshop but I understand that many people don’t want to go that route.