In micros, this will happen as well. Not only in Freerolls.
Key words here are: Early stages mtt.
What to do? Shove it and get a stack or get out and bust looking like a maniac...
Having around 50BB is plenty to play a good game. You just need a good RFI strategy if the post-flop seems difficult to play.
During the early stages, you need Flat and 3-Bet ranges as well in order to avoid tricky situations.
There are little interest to steal. Blinds are irrelevant when thinking about open ranges to steal blinds.
The best you are post-flop, the looser your opening ranges are.
Draws, top pairs, etc usually put recreative players in bad positions with check raises and all ins in hopes it gets there. Construct a solid pre flop open range and stay away from marginal hands play, this will make your tournament life much longer.
Of course, there are moments where you will have to face it. But never do that with stacks around 40-50 BB. Not necessary in my opinion.
Be solid early game, construct your image on the table, understand your opponents strategy and tendencies.
So, I think that for freerolls it is understandable. This happens often and we sometimes do fold with better hands. But the tournament life is more important and knowing how to approach each stage, makes your life much easier.