Yes, the sectors are in a block, so there are gates to control programming, but the block as a whole goes "offline" when programming. I can't believe they fail to mention that - you are not the first one to miss it.
From the RM:
"The MCF51QE128/64/32 flash memory is organized as two 16-bit wide blocks interleaved to yield a 32-bit data path"
Since it needs 32 bits, it need both blocks.
If you get the code from that sample, post it here if you would.