Disadvantages needn't be bought off all at once, they can be gradually lowered or reduced to slightly less unpleasant disadvantages.
Example: Paying off a big Enemy:
You go on an adventure and kill your enemy, the evil Doctor Zark, who was worth 20 points when you got him. However, you only have 12 points total at the end of the adventure. So, you spend 10 points and reduce (but not eliminate) your Enemy disadvantage. Now, your enemy has become Dr. Zark's 14-yr old evil whiz-kid nephew, Dweezel. You could then go on another adventure where you kill Dweezel, spend 5 points and now you have a 5 point disadvantage that is essentially a -2 reaction modifier amongst all evil geniuses: "Stay away from that guy, he killed Dr. Zark and his evil nephew!" If at this point you wanted to buy off the 5 point reputation disadvantage, you would need to do something to win the good graces of the evil genius community. Say, a large donation to the local evil planetarium, or some such.