Are you sure it was from Christian Science and not the Christian Science Monitor which has been a long-time sponsor (and if I recall occasional reporting partner) of NPR.
Are Christians not also listeners?
It sounds to me like you are disappointed that the liberal bubble isn’t as thick as it could be. That even accepting supporting money from the bad people is compromising.
It seems that you are implying that the sponsors of NPR get a say in their programming and reporting? Seems like that is the thing I would be upset about, not that the “wrong people” are supplying the money.
They were founded by the same woman, Mary Baker Eddy, like a century ago, but today they just have one specifically-cited Christian Science article in each print.
It seems they may have the same owner still, but seems like they very much have editorial independence, judging by the things I read.
The Christian Science Monitor is a well-respected newspaper associated with the church. The few times I've read a paper copy, there was usually one editorial with a religious theme. Their religion did not otherwise color their reporting.
I am not the least bit suprised that the Christian Science church might support NPR. Demographically, Christian Science members probably have very high overlap with NPR listeners. And they are, after all, a church which is best known for being associated with a newspaper. I would not be the least bit surprised if they donate to NPR mostly because they want to support public radio.