If I keep the ADC in freerunning mode no other code will be executed because the ADC interrupt always triggers to collect datas, fills up the value in the registers, and triggers the next conversion.
Why do you think that? There is 110us during a conversion that can be used by
the rest of the program, before a conversion complete interrupt fires.
The normal way of using the ADC in Arduino runtime is not via interrupts, but to set a single
conversion going and busy-wait for it to finishd - that really does waste a lot more CPU time.