"And then years later make someone adding a feature lose his hair trying to figure out why adding some serial computations made the timer imprecise."

If code is properly commented this type of situation should never arise. You could use the same argument with any time critical code.

"While I am adamant on short ISRs there may, indeed, be a case for an ISR more than 250 cycles in duration."

In which case make the timer interrupt the highest priority.