Pope Francis addressed Congress as an important global spiritual leader, but also as the head of state of Vatican City, which is technically a sovereign, independent state. So he is an 'outside' voice.
The purpose of the separation of Church and State is to avoid any religious discrimination or favoritism on the part of federal or state government. Remember, the Consititution (including the first few Amendments) was written in the late 18th century, when the historical backdrop featured protracted religious war in Europe; when Britain herself had an established state religion, Anglicanism, to which many of the Founders did not adhere; and when the various Colonies forming the new nation had very different religious traditions. (Puritanism was important in New England; Pennsylvania was associated with the Quaker faith; while Maryland was founded by Catholic gentry and their Anglican servants, with the latter group eventually overturning the religious toleration of the early decades to 'establish' an official state Anglican church.)
The federal and state governments are to avoid endorsing any one religion, however popular it may be among the American population at large. There's little hint that, in allowing Pope Francis to address them, Congress was officially 'endorsing' his faith. Therefore, the 'wall of separation' wasn't breached by his address.