Can kusala ever come with dukkha? How come in real life sense restraint

In this case you mention there could be many scenarios.
Genuine sense restraint - i.e kusala citta- always comes with pleasant or neutral feeling as you say.
But there can easily be a kind of "sense restraint’ In the way of metaphorically gritting ones teeth and just enduring - so as you suggest dosa mula citta in that case.

Also cittas arise and pass away very quickly so there might be moments with dosa and moments with genuine detachment and then moments of desire and so one…In fact that is the way of daily life…

Also see this thread. Issues with meditation - strange experiences, unpleasant feelings: advice

As you know mere effort and good intentions alone are never going to work. It is the understanding that always comes with detachment that is the real path.