One of the likely reasons behind all this is that at the time the contracts were written, no-one expected MW1 and MW2 to become such huge hits. COD2 has sold nowhere near as much as even MW1 and it's probably beaten by its sequel now. It's also been reported that Activision was actually against moving the franchise into a contemporary setting - which is probably why IW shares rights to this incarnation (but not to the COD IP itself).
To put it simple - royalty percentages are probably quite high, which means everyone at IW would get a lot of money from the sales (instead of the publisher). It would also make them far more interested in taking their time with the next iteration and not letting anyone else work on it. But Activision wants another MW pronto - so now they're trying to "re-negotiate" the contract this way. There's even word about them presenting an impossible situation to make the founders act in an "insubordinate" way, by trying to force them to fire a certain amount of employees.
I understand that Activision has funded the development of the franchise and its their investment. But it shouldn't allow them to take control of the IP and the actual people behind it in this way.