I copied this from an faq on gamesfaq.com. Hopefully it helps (I used it to get through the 2nd Scarecrow encounter).
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This sequence will be similar to the last but there will be one chief
difference. Scarecrow will no longer rotate in a full circle. Instead, he will
simply shift his gaze back and forth between two points slowly. This means you
have to time your movements better.
Wait for him to move away and then jump the gap to the right. You should have
time to run past the lower cover and just hide behind the statue instead. There
is no cover to be seen from here though. If you look up above however, there is
a crate that can be used. Select your Batclaw and target it. Pull it down and
then when it's safe to move, run over and hide there. From here, repeat the
process and pull down another crate. Wait for Scarecrow's gaze to move to the
left before running here. Wait again to climb the following ledge.
Take this path down some stairs to a fight with skeletons. Just stand at the
far end and wait for them to come to you. You can see at that end where they
appear, the light of Scarecrow's sight. If you step in there, he'll see you. So
it's better to stay back, this way the constant movements of Freeflow Combat
don't accidentally carry you into a fast demise.
Wait for them and they won't fight you any differently than thugs. Strike,
Counter and so on. They're pretty weak actually so it should be no problem.
Wait for Scarecrow to move, then proceed.
Climb up the wall and wait here. When his gaze comes all the way to the left
toward you, wait. As soon as he moves, make a run for it. Jump the gap and
shimmy around here. Either just hang on the ledge or try to climb up quickly
and take cover on the other side. Wait, then jump the gap. Climb up the ledges
here to the top.
Wait here until his gaze goes past you and to the left. After that, jump this
gap and climb up to shimmy. You need enough time to shimmy around the corner
and if you moved right after his gaze passed over you, you should be fine.
Hang on the ledge that has Batman's back to the camera and wait for him to pass
by again. Wait patiently for him to go back to the left before shimmying all
the way around and dropping down. Proceed quickly up the next path for another
fight with the bone crew.
After defeating them, climb up the following wall. Grapple up to a high ledge,
then jump to ledge that you need to shimmy on. Pull yourself up when it's clear
and look at what's ahead. Besides dodging Scarecrow's vision, you also have to
worry about the pendulum. It's best to move when Scarecrow is looking toward
you and then moves the other way. Jump to the next platform, then wait a second
if you need to (you'll have the time) for the pendulum to move, then jump
again.
Wait on this next platform and hide. When Scarecrow's gaze soars over you,
climb up and run all the way down this platform to the bottom and hide behind
the short wall here. Just wait for his gaze to pass back over you, going left.
Once you're clear, run to the right, hop the small barrier, climb up, and jump
the gap to reach the bat signal. If you get a little caught up, hide before
climbing up. Get to the signal and put an end to the nightmare.