Shrink segments to fit alignment instead of throwing them away

We risk throwing an entire large chunk away if it is just slightly
unaligned which then causes the crash kernel to run out of RAM. Keep
them and shrink them to alignment.

Signed-off-by: Hongyan Xia <hongyxia@amazon.com>
Signed-off-by: Simon Horman <horms@verge.net.au>