From my understanding the card is similar to Switcheroo where if the second target is no longer existing the spell will fizzle.
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Rites of Reaping will not fizzle, because some of its targets are still valid. The spell will only be countered if all of its targets are illegal. Instead, the spell does as much as possible, which is to give +3/+3 to his creature. This is defined by 608.2b.
Your probably came to the wrong conclusion because your understanding of what happens with Switcheroo is incorrect. It won't be countered (fizzle) if only one of the targeted creatures disappears. However, it won't have any effect either. An exchange requires something to be received and something to be given, so it cannot happen if one of the two targets is illegal.