Does the Bible suggest that there would be a literal apostasy of the early Christian church? In 2 Thessalonians 2:3 and Acts 20:29 I interpret them to mean that there would be a literal apostasy of the early Christian church or is there another meaning to them that I am missing?


  2 Thessalonians 2:3: Let no man deceive you by any means: for that day shall not come, except there come a falling away first, and that man of sin be revealed, the son of perdition;
  
  Acts 20:29: For I know this, that after my departing shall grievous wolves enter in among you, not sparing the flock.
In traditional Christian theology, Apostasy, yes.  Total Apostasy, no.  

The first verse is commonly understood to be part of end-times prophesy.  There is no indication that it relates to the early Church, and to try to make it fit there ignores the context of the surrounding verses.


  3 Let no man deceive you by any means: for that day shall not come,
  except there come a falling away first, and that man of sin be
  revealed, the son of perdition;


The "man of sin" a.k.a the "son of perdition" is commonly believed to be the Antichrist.


  Matthew Henry's Concise Commentary on 1 Thessalonians
  
  2:1-4 If errors arise among Christians, we should set them right; and
  good men will be careful to suppress errors which rise from mistaking
  their words and actions. We have a cunning adversary, who watches to
  do mischief, and will promote errors, even by the words of Scripture.
  Whatever uncertainty we are in, or whatever mistakes may arise about
  the time of Christ's coming, that coming itself is certain. This has
  been the faith and hope of all Christians, in all ages of the church;
  it was the faith and hope of the Old Testament saints. All believers
  shall be gathered together to Christ, to be with him, and to be happy
  in his presence for ever. We should firmly believe the second coming
  of Christ; but there was danger lest the Thessalonians, being mistaken
  as to the time, should question the truth or certainty of the thing
  itself. False doctrines are like the winds that toss the water to and
  fro; and they unsettle the minds of men, which are as unstable as
  water. It is enough for us to know that our Lord will come, and will
  gather all his saints unto him. A reason why they should not expect
  the coming of Christ, as at hand, is given. There would be a general
  falling away first, such as would occasion the rise of antichrist,
  that man of sin. There have been great disputes who or what is
  intended by this man of sin and son of perdition. The man of sin not
  only practises wickedness, but also promotes and commands sin and
  wickedness in others; and is the son of perdition, because he is
  devoted to certain destruction, and is the instrument to destroy many
  others, both in soul and body. As God was in the temple of old, and
  worshipped there, and is in and with his church now; so the antichrist
  here mentioned, is a usurper of God's authority in the Christian
  church, who claims Divine honours.


And Acts 20:29 is understood to be speaking of those who claim to be Christian, but preach a false gospel, which has been happening since the early Church, and continues to this day.  It does not speak of a total Apostasy, it speaks of people being led from Truth into false doctrines. 

A Catholic rebuttal is found here.

A Protestant perspective on what to watch for, as far as these ravenous wolves are concerned can be found here, along with an orthodox (small "o") view on Apostasy.

And as God is not a liar, there could not have been a total Apostacy.  

He Himself promised that he would always keep a remnant - there would always be those who walk in His truth.  A Total Apostasy is impossible, because God himself promised it, and His power is enough to prevent it.

At least that's how "Mainstream Christians" see it.