I don't know of anything that can be done with the liner in

As Al said, just wait until you need to replace the liner and then address the rust issues.

When we're replacing a liner and the walls have rust, we scrape the rust off and clean the area, Then we put Rustolium on the effected areas (the company I worked for in Va. used spray on galvanizer - which for all I know was just gray spray paint ) The final protective measure is to put wallfoam on the walls - even if they rust out again, you've got an 1/8" barrier between the rust and the new liner.

HTH - Ted