Scanning using a professional scanning fluid like Kami along with a clear overlay material like DuPont C-42 will go a long way to minimize surface problems in a scanned neg. You either need a special film holder or a drum scanner to to that though, and it's a messy pain to work with if you've never done it before.
You may be able to help your cause out using the Channel Mixer. Use it as an Adjustment Layer and blend a percentage of the good channels into the bad one(s). There's a good chance that will cause a color shift, but that can usually be dealt with by other means.
Take a copy of the file and convert it to Lab color. Look at the "a" and "b" channels. If some of the damage resides in either of those channels, you can often apply a liberal dose of Gaussian Blur - something like five to seven pixels to either or both channels and fix your problem without any undue effect on the overall image. I usually would do that to a duped background layer and be prepared to mask off any super saturated areas that smeared from the blur. If, in fact, the Lab trick helps, then flatten your image and paste it back on top of your original. You can then toggle it on and off to see the improvement.
You may never avoid all manual labor on this, but you might avoid some.
