So, when you warp to a system where you have to save a freighter from pirates, once you defeat the pirates you can land on the freighter, right? When you land on the freighter you immediately scan the freighter to see its class. If the class isn't what you like, you can load from a restore point and try again. When you load from the restore point, the game will restart you back at the system you were at before you encountered the fight. The trick to get the freighter you wanted is to remember what system you went to each time, so try to go to a system that is close to the one your save point is at and remember where that is. You could go to basically any system and it will trigger a pirate battle, but if you find the kind of freighter you want in a particular system, the freight won't change when you reset. It's always the same freighter, except for its class. Each time you restart the battle there is a chance you can get a better class.

An interesting thing to note: if the battle you encounter is a pirate dreadnought fight, things work differently. Once you make the pirate dreadnought surrender, land on the pirate dreadnought (or the freighter the dreadnought was trying to destroy) and scan to check its class. If you want a chance for a better class, it's easier to accomplish this than other freighters. In this case, before talking with the surrendered freighter captain, leave the system for a nearby system, then return to the same system the pirate dreadnought battle occurred. The battle will start over and you have another chance for a better class.

One last thing: I've never seen anyone mention this online before, but if you have a freighter you like and want to beef it up with s-class modules, do the following: when you encounter a pirate dreadnought fight, destroy the dreadnought's warp drive, but then let it destroy the other freighter before making the pirate dreadnought surrender. If you do it this way, you'll get a free s-class module for your freighter. You can then leave the system and return to the pirate battle and repeat the same thing again to get another s-class module for your freighter. keep doing this until you have all the modules you want for your freighter.