All the Sectopods, including captured and MkII, have exactly the same armor values, the difference is that the MkII has an area effect laser weapon which is far less effective against heavily-armored targets (and Sectopods are the most heavily-armored out there); it's great against groups of weaker aliens, and its laser is effective against the Colossus. Also, Sectopods are weak against lasers, and their Sectopods are armed with lasers while yours doesn't have a primary laser.
The reinforcements usually just land right in the middle of things and get chewed up; they're mostly to draw fire
Big hint if you're having trouble: If you don't think the MkII is worth it, you should probably stay away from it, because as soon as you activate it, the aliens send in a *huge* force of reinforcements to compensate. They *really* want that thing dead. I agree that the Sectopod could use a more powerful non-AOE weapon, so I've increased its cannon damage significantly (60 -> 100, but it's still doing armor-piercing damage--still less effective than lasers against other Sectopods). I put the change in the current version online.
Another hint: The captured Sectopods are not re-patriated until the aliens breach the base, so if you can slow them down... Or, you can even try to take out the captured Sectopods before they're activated.