Then again, regarding your questions:
First of all, yes, the restart command technically erases all that you have on a character, whether it's money, ship, equipment and so on, so seeing that you don't want to lose those, it would be a bad choice. Still - just in case - if you are fine with losing the ship and equipment, but keeping the money, you can do that by:
-creating another character
-sending the money from your current character to the newly created one
-restarting this current character
-send the money back from the other one
Alternatively... a way to adjust your reputation in order to become friendly with the Zoners (and buy their ID) is trough bribes. All Freeports and most Freelancer stations, as well as some corporate stations have Zoner bribes, which will increase your reputation with the Zoners.
I hope this helps, but feel free to come back here if you need anything else.