Zeus explains this himself, in the final scene of the movie:
But now the world knows a man can stop him [Hades].
Of course, you had some help.
A sword, the Pegasus...
I wanted men to worship us again, but I didn't want it to cost me a son.
So, he simply didn't want his son Perseus to die.
It think Zeus has also some regrets, and feels partly guilty for the loss of humans' worship:
You may not want to be a god, Perseus but after feats like yours, men will worship you.
Be good to them.
Be better than we were.
Last, but not least, Hades is not serving him:
Zeus must think I serve him but I am growing stronger.
Until I possess my full power you will be my weapon.
Zeus probably realized, at some point, that human fear fuels Hades' power, but not his own, and thus realized Hades' plan to overthrow him.