Look. Execution is inhumane. You can't make it gentle, peaceful, or nice. All you can do is make it quick, which it sounds like they failed to do here. But if the good people of Alabama aren't comfortable with someone struggling for half an hour and then dying, they shouldn't execute people at all.
That said, the person quoted in this article is the executed's spiritual advisor. If I was Smith's spiritual advisor, I'd also be claiming the method was inhumane, violent, and awful. The reality is that it's a lot more cruel that Smith went back into the execution chamber despite them botching the job the first time than that they half-assed the nitrogen asphyxiation. It was an untested method, but every method of execution has a first person to be executed with it.
If your society is bickering over which way it should kill the condemned, you've already ceded the moral high ground. We have already solved execution, and we've had it solved for decades, even centuries arguably. Hanging, firing squad, electrocution, beheading, lethal injection--every method has its proponents and detractors, but every method is to the same end. If you're too squeamish for what happened in Alabama, an alternative method of killing people isn't going to fix that for you. The solution is staring you right in the face, and it's life without parole.