Edit: That must be it. We just got a block that packed up over a thousand of them (block 350476) and my CPU load is back down to something near normal.
CPU usage was probably from running your own validation on the new block and not the size of the pool.
If the unconfirmed tx pool gets too large, does it do something which doesn't scale?
If it gets really large, you can have some older/lower fee/unconfirmed transactions being dropped from the mempool.
The clients that sent that transaction may still retry and add it back to the network by broadcasting it again.