It's not exactly a definitive answer for running with smoke launchers but I personally take this answer from the Eldar
FAQ to suggest it's perfectly possible.
Q. The Star Engines description says the vehicle may move an extra 12" 'in lieu of shooting'. Does this mean that they cannot make this extra move if they are unable to shoot for other reasons (such as being shaken). Also, when is this move executed - in the Movement or the Shooting phase?
A. As long as the vehicle is allowed to move that turn, and does not shoot or embark/disembark troops, it may use its Star Engines. This means that it can use them when shaken, but not whilst stunned. This extra move of up to 12" is executed during the Shooting phase.
Per the deployment example on page 93 for the Dawn of War mission type, an
IC may deploy with a unit inside said unit's dedicated transport.
edit: Thought I should just point out that smoke launchers aren't done "instead of shooting" per se but at the end of the vehicles movement and simply prohibit shooting, making them equate to something like shaken in the eldar vehicle example, if both were actually done in the shooting phase as a replacement for shooting, the situation might be a bit different.