Yes, limiting the tasks of the ISR to a minimum is a good idea.
I have built a true RMS meter for the power-line. All the code is written in C, except for the timer ISR. This routine, written in assembly language, reads the samples from the ADC and put them in a table (only one sample per ISR execution). When the last sample is in the table (32 samples have been taken in one power-line period) the ISR sets a flag, so that other routine proceed to computations. And it works properly.

Alfredo del Rio.