He knew he was a holding Alec back and didn't want to be a burden. The black magic guy was specifically targeting Loneal meaning Alec had to focus on protecting him rather than himself or attacking. Loneal has little ways to protect himself as he's got a weak constitution.
He knew he was about to fall unconscious (he said asleep but I took it more as fainting) which would be an even bigger problem for Alec so he removed himself from the equation so Alec could protect himself. He knew the seal was below the cliff because he heard the squeak and just trusted it would pull his unconscious body out of the water.
I didn't fully understand it until I read ch 42 either... very subtle and implied. And poor Alec knows none of this...
what is going on? why did he jump