In a craft consisting of a thermal nozzle, am reactor, am tank and control pod engine will force turn the reactor, when it is activated. Is this working as designed? If so, is it possible(as in can I submit a patch) to change this behavior, so the engine respects reactor setting and does not turn it on accidentally?

Yes is working as designed that the a reactor is activated when the nozzle is activated. It is to make it easier for casual player to use KSPIE.