Well, what would be the evidence of such tampering though? We'd have to find other, older manuscript traditions that didn't have those words, and then maybe we could conclude they are not original. I'm not aware that any such MSS exist.
But I think the evidence leans against tampering, because as you can see from the original passage (linked above), there is not just one throwaway reference to Rome but a whole line of Irenaeus's argument. He goes on in the same chapter to enumerate the bishops of Rome after Peter and Paul were there...Linus, Cletus, Clement, and on and on. He basically says that the Apostles appointed people in a direct line right down to the catholic Church (and yes he uses those words) of his day.
So if this reference to Rome is forged, then it's not just a matter of two words.
Since Irenaeus wrote decades after Ignatius, how come Irenaeus doesn't call the Church in Rome "the Catholic Church". If it was so well known as such then how come its proper name as the "Catholic Church" is not used by Irenaeus or other writers until the 4th century.
Also don't forget that before the ink was dry on the epistles that Paul wrote there were people corrupting his letters, making spurious copies and trying to pawn them off as legitimate. While God promised to look after His Word [the writings of Paul, et al], He never promised to do the same with those that followed the apostles.
We also know that Origen was a skillful corrupter of Bible texts. What makes us think that he and others like him weren't also corrupting the writings of patriarchs such as Ignatius, Irenaeus, and others that were not under divine oversight