Before discussion gets started, I'll point out the difference between the two. Scientists generally can't set out to falsify a religious claim without proper evidence. I'm not saying it doesn't happen, but it's not in their interests unless they actually can disprove it. Because if a scientists bends data to make a point, other scientists can make their careers on proving him wrong. It's a self-correcting system.
The only widespread scientific misuse is that funded by religious organizations to "get science on their side." Right or wrong, fudged data or not, they'll print something that bolsters their cause unless it's instantly recognizable as fabricated (though even that rule is tenuous, since some do publish such laughably false material).
Human bias exists, and evidence can be overturned. But science with an agenda has consequences in the form of risking exposure to your unethical methods. And also exposure to repeated tests from other sources, which always take place before conclusions are drawn, and which will find different results if you fibbed to make a point. Religious "science" is not inherently self-correcting, it's self-serving, and therein lies the difference.
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To answer your question, it's a subjective question to ask which is more unethical. They're both unethical. That's about as far as we can reliably claim.
I just needed to get my two cents out up there, lest this thread turn into an attack on the scientific process.