PWM Ground Modulation: is this circuit going to affect my other ICs?
other points fixed by question update


the IN2/OUT2 opamp is used as comparator (not recommended with the LM358)


That's not recommended because amplifiers that aren't meant for comparator applications can latch-up. Also, adding a bit of hysteresis sounds desirable, so that slight supply or temperature voltage variations don't lead to a flickering LED if you're close to the threshold temperature. Look for Schmitt trigger circuits.



Your schematic doesn't tell us how stable your ground is, but usually, a slow PWM like the one you're using here, switching a low current like what is necessary to drive a fan shouldn't really be a problem.