Interesting thought experiment. :thumbup: The rest of the post is just my thoughts about it.
Simple answer: Don't burn all the thrusters at the same time.
For the sake of keeping it simple, let's say that we have a ship with two thrusters, one with an x amount of ISP and the other with x/2.
I think that it's more complicated than just taking the average ISP.
There are some distinctions that have to be made, for example are the thrusters burning from the same fuel tank or does each thruster have it's own tank(s)/propelant?
If it's the second case then the answer is simple, you burn the thruster with the higher initial mass/final mass ratio first and then the other one, this way you get the maximum dV from the available fuel. (When you burn the second thruster, you'll have less mass to "move").
Now arises the question, what if they have the same initial mass/final mass ratio ? In that case, it doesn't really matter which one you burn first. The total dV you'll get will be the sum of the dV each thruster can produce.
In the case that they burn from the same tanks, for the same amount of fuelmass:
A thruster with x amount of ISP will give you a y amount of dV.
A thruster with x/2 amount of ISP will give you y/2 amount of dV.
So, it would be better to burn the thruster with the higher ISP longer, than burning both of them at the same time.
Now, suppose that you did burn both engines at the same time, what would be the total dV you'd get?
Well... things get complicated at this point, since we have to calculate how much fuel the lower ISP thruster would burn -during the burntime of the higher ISP thruster- and then subtract the fuelmass (of that burntime) from the higher ISP one; and keep repeating the process untill the values converge.
Newton's method
Things would be simpler if you had thrusters with different thrusts but the same ISP.
I hope this post helped.