Good points there. Add to the mix the likelihood that Balon probably started rebuilding the Iron Islands fleet from day one to get it to the current state it was in A Game of Thrones. No restrictions on and monitoring of the fleet? This is a fleet and people that for centuries have pestered the mainland.
Keep in mind that they had destroyed the Iron Islands fleet and invaded the islands themselves. This was not some negotiated peace, it was the aftermath of a bloody war that, despite victory, cost the mainland ships and men and probably added to the kingdom's debt load. This was a total surrender similar to Japan at the end of WW2, after, like Japan, the Greyjoys launched an unprovoked sneak attack. Robert may have had a forgiving nature, but this really should have tested even him. Greyjoy did not surrender until it was all over, as compared to say, immediately after losing the fleet, but before the island invasion. While Cersei's suggested genocidal "mountain of skulls" approach is on the other extreme, some sort of ruler change was in order.
Tywin Lannister would have likely advocated for something like you suggested, at least something for more consequential than what Robert did, which was basically nothing. Only one hostage? Why not one from every major family on the Islands? They all participated in the rebellion, just the way the Riverland lords rebelled with Robb. [although, just checking right after posting this, it seems there was at least one other hostage -
http://awoiaf.westeros.org/index.php/Baelor_Blacktyde]
And Tywin's insistence may be one important reason why Robert
didn't do as suggested. While only ~5/6 years into his marriage, things may have started to go sour with Cersei and the Lannisters by this point and Robert did not listen to Tywin out of spite. A stupid move and one I would have thought Eddard and Jon would have modified.