Warp lightning cannons can kill everything, true. However, Skaven have other weapons to attack knights and infantry. A single rank of knights is a bad target for lightning cannons, as only one is hit unless you land the template on them. Unless you have ranked up knights, who eat a warp lightning template, the best target for them on his list is a Steam Tank. I have little experience vs skaven however, so If this generally isn't in their line of thinking I wouldn't know.
No they likely won't kill it in one round of shooting, but they're likely to do D6 wounds, greatly reducing its effectiveness. It may be best to screen the tank so he can't optimally place a shot.
Ty for clarification on shooting into slaves. Once you're in combat, everything is safe. So the issue is balancing effectivescreening for your Tank(s), and getting them into combat quickly.
Captain on peggy is fantastic, esp with the charmed shield. Without jezzails or a BS shooting weapon on any character, the charmed shield can save him from the cannons. Even if he kills the captain, he's not killing the steam tank.
Life magic is the 2nd best lore for empire behind light. IMHO. With a halberdier focused army vs skaven it may be #1. Dwellers will cut one of his units in half before combat, and flesh to stone will prevent the wind mortars (and doom rocket) from punching big holes in your forces.
Demi's are nice b/c he likely only hits one with a cannon. 2/3 chance to lose less than 60 points, isn't bad. They will also tear up the ratogres. On average 21 rat ogre attacks do 2.28 wounds to demi's. A unit of 3 Demi's does 5.9 wounds(if they don't lose a model, knights are I3, ogres I4. A unit of 4 demi's with a champion kills 2 rat ogres, and remove steadfast. You can break this unit on the charge. Since his unit costs over 300 points, this is a fantastic match up, as it prevents the ratogres from ripping your infantry apart. It also allows your Tank to have a safe, unbreakable, combat vs his infantry.