When I play with my friends, we do what you propose; we count the IPC value of a country at the end of its turn. We find this to be simple because we simply count the IPC difference for each territory, and add this (or subtract) from the default IPC for this nation.
We find that when we adjust the tokens for all countries, that this is a very error prone method, and it forces us to do counting that is not necessary. All that is necessary is to know how much your nation is worth at the end of your turn. At all other times this information is useless.
But, you should still use paper money, because you collect money at the end of your turn, and you may also have saved some money from your previous turn phase. The amount of money that you have in pocket is generally not the same as your IPC value at any given moment in the game.