InnoDB maintains two checksums per buffer pool block. Old formula of checksum, and new formula of checksum. Both are read, both are written. I guess this had to be some kind of transition period, but it obviously took too long (or was forgotten). Anyway, disabling checksums code entirely makes single-thread data load 7% faster – though in parallel activity locking contention provides with some extra CPU resources for checksum calculation.
Leaving just single version of checksum would cut this fat in half, without abandoning the feature entirely – probably worth trying.
Update: Benchmarked InnoDB checksum against Fletcher. Results were interesting (milliseconds for 10000 iterations):
So, though using Fletcher doubles the performance, -O3 optimizes InnoDB checksumming much better. How many folks do run -O3 compiled mysqld?