First, that is very nice of you to help the orphans in Kenya.
So, your friend, not you, is helping with the orphanage. You are merely gifting your friend money. But you could be subject to gift taxes. For the annual limit you can send to anyone as a gift for 2016 and 2017 is $14,000 per year. So if you only sent $10,000 a year, you are fine. It is a gift and it's under the limit.
Now, you cannot deduct this $10,000 if it is truly a gift. Since the organization is in Kenya, if it is a charity and you would want to treat it as a charitable donation, one would have to research if the US has a treaty established with Kenya.
So as long as it's a gift and you did not exceed $14,000 for the entire year, you will not have to worry about reporting it as income but cannot claim it as a deduction.
I do think the IRS misunderstood you and probably thought you were running the organization. It seems like you are merely a person gifting the orphanage.
But again, be careful about possible gift taxes.