Ion cannons dont ignore termie armour, but you shouldnt have a problem with deep striking GK termies.
Keep your army close together and dont give them terrain to use to hide when they deep strike in. Sure, they can fire, but thats not the worry: the worry is assault, and they cant do that the turn they deep strike.
I played a 1k point game against deathwing. Two squads deep striiked in one turn. Out of the 11 termies, one was left standing, his commander, who was killed after he couldnt persue the FW squad he persured and my shas'el (sh'utor sch'ank =p) melted him with his t/l fusion blasters.
just take some suits with plasma rifles, and be paranoid and in position every turn: buy the multi tracker on your tanks and keep them moving so theyre hard to get at
another strat is to devide your army into a number of spread out groups, each concisting of at least one crisis team and some fire warriors. Use the above tactics (melt them the turn the DS), and then theyre left with a huge expanse to footslog through while you shoot them up.
take full advantage of the termie innability to sweep (volantary fallbacks can spell doom for termies. much doom.)