If I play Icathian Rain and my opponent retreats two units leaving only Fiora, am I forced to target Fiora 6 times and pay 6x Deflect/recycle rune costs?

You must target Fiora all 6 times (she's the only legal target), but you only need to pay Deflect costs for enough instances to deal lethal damage. For example, if Fiora has 4 Might, you must pay Deflect for 2 instances (4 damage = lethal), but you can decline to pay Deflect for the remaining 4 instances, and those damage instances will not resolve.