Big noisy distraction while someone slices in, sets up a few parameters, and then 20 minutes after you're "driven off" the reactors go critical.
Or, hell, vent the reactor, so now the star destroyer's sitting in space, with only what emergency power it has available, so no shields, no weapons, no hyperdrive...
Other amusing things you could try (with adjudication required)...mess with the hyperdrive so it turns on and off randomly. Have the sublight engines overload and burn out, possibly explosively. Or hack a shuttle so it goes into hyper in the landing bay.
Now, realistically (and I know, we're talking about Star Wars here), boarding actions are going to be a fact of life in naval warfare and such things will be known about and defended against. But no defense is perfect.