This was something that I had considered while reading through the Beta rulebook. The Obligation section of the chapter on character creation recommends that group starting application be between 60 and 70. With this in mind, I've had the following idea (It hasn't been tested, so I don't know how well it would work):
Keep track of the character's relative obligation on the character sheet. By relative obligation, I am referring to what they have beyond the starting obligation. For example, a character may start with +10 obligation in exchange for +10 XP, and I would have the player write "+10 Obligation" on the character sheet. If that same character reduced his obligation by 15 over several gaming sessions, I would have him change the character sheet to say "-5 Obligation."
Then, you would choose a base amount of obligation for your group between 60 and 70. This amount would be static, no matter how many players are in your group. Then, you would divide the base obligation by the number of players currently in your group and add each player's relative obligation.
Example: Your first session consists of four players, two of them have taken extra obligation during character creation. Joe has taken 5 extra obligation for 1000 extra credits; Fred has taken 10 extra obligation for 10 XP; and Jim and Bill have both decided not to take any extra obligation. You have decided to set the base obligation at 60. 60 divided by 4 is 15, so each character is assigned 15 base obligation. Now Joe has 20 Obligation, Fred has 25, and Jim and Bill have 15. The total group obligation is 75.
Several sessions later, two of your players have paid off some of their obligation, but you also have two new players (Tony and Sam) that have joined the group. Both Tony and Sam have taken 5 extra obligation during character creation for extra credits. Joe and Bill have both settled 10 obligation during the previous sessions. Now the relative obligation numbers look like this: Joe -5, Fred 10, Jim 0, Bill -10, Tony +5, and Sam +5. The base obligation would still be 60, but this time you would divide it by 6, so each character would have 10 base obligation. You will notice that Bill's total obligation would be zero after the base and relative are added together. The book recommends that a character should not be able to have less than 5 obligation, so he will default yo 5. After adding the relative obligation, the totals would look like this: Joe 5, Fred 20, Jim 10, Bill 5 (default), Tony 15 and Sam 15. This is a total group obligation of 65.
The base obligation of 60 would be static throughout the entire adventure, but relative obligation could change by quite a bit. Again, I have not tested this, so it could be rubbish; however, it seems like it could work for your situation. The group is not overly penalized for adding or removing players. In this case, the group worked to pay off 20 obligation over several sessions, but the two new characters brought an additional 10 obligation through character creation.