maybe a bit late but u may take a look at the FLHook project

it got a lot of admin-commands .setrep and even commands for editing money (.getcash,.setcash and .addcash) ... also playercommands, its opensource so u or anotherone with some c++ knowldege should be able to create new polayercommands like /setreputation <faction> <value> using these still aviable admincomands:

first .getcash to prove that the player have money thats needed
then .setcash to lower the money value
then .setrep to set the reputation
then maybe some nice text to the player by .msg <player> <text>

if u not like to recompile flhook u can also programm your own php-website that communicate with flhook and send the needed commands via telnet, well then u have to secrure the page by a personal login and assigning playerchars to page-accounts to make sure no one edits other players.

an exteded fl-hook is maybe the answer but flhook can't edit players that aren't logged in on the fl-server, it lacks the routines to open charfiles and edit them like ioncross, it 'just' manipulates values inthe servers memory.

to get it working u have to patch the server first using the 1.1 patch from M$