Although the running board isn’t affected yet, rust spreads rapidly, and underbody rust typically worsens more quickly than visible rust on the surface. Hence, it is crucial to have your mechanic inspect the extent of rust - check inside the sill, floor pan, and suspension mount area to ensure structural integrity. Ensure that the rusted portion has been cut out completely, and new sheet metal is welded in place. Also, have the area treated with rust-proof primer and sealed with underbody coating.
Any trusted body shop can do the job, and you need not get it done at the authorised service centre since the quote is exorbitant.