Perhaps but the same could be said about many other ults. Like, for example, Ryze ult. You could say "Oh if an enemy jungler comes, he can just ult to escape."
In the case of Mordekaiser's ult, it times out eventually, the ally needs to survive long enough to exit the ult, which actually isn't as hard if you focus on dodging rather than dealing damage. Keep in mind the jungler can see where the two will appear, and will immediately be able to attack and help once the ult is done. The jungler is most definitely useful if the timing is right, not just with Morde but with all champions. In this case, you'd need the jungler to gank once it's unprofitable for Mordekaiser to ult you. For instance, if his health is down to half, and where you could kill him if he ults you. So request a gank if his ult is down or his health is relatively low.
Mind you, this also affects him. He can't ult you during a gank cause it will cut off his jungler. + He can't jungle because if he ults you, he cuts off his allies. Which is really beyond me, I've seen so many Mordekaiser's attempt to do this, and I'm like.... why lol.