First off: this is a secular site. Owned and hosted by a secular company. That said, it is also a Christian site in the sense that it is a site about Christianity and populated by Christians.
Non-Christian questions are fine as long as they genuinely seek understanding and/or information. Caleb excellently goes into more detail in his answer to Is critical analyzing of Christianity allowed here?.
This has already been covered to some extent in Should we be deleting blatantly non-Christian answers?. Wax's answer makes a good point that the community has a significant amount of power, and Waggers sets out a few ways to deal with non-Christian answers. Usually, those are our options for dealing with answers that claim to provide a Christian perspective.
In this case, we have two posters who answered claiming to speak from an atheist's perspective. Not only is this against the spirit of the site, it's also against the question itself! The second half of the first sentence is:
I am very interested to get the Christian perspective.. Hence, I believe that deletion of answers from an atheist's perspective is fully justified here.
Now, I will note that not all atheist's answers should be deleted. Marc Gravell is an atheist, but he has given multiple high-quality answers. The difference is, when answering he has legitimatly tried to represent a Christian viewpoint or at least followed suit from the question. It shouldn't matter who the author is so long as their answer fits the site.
As Kaz Dragon put it so well, we (the community) seek to restrict the viewpoints of answers, not who can answer.
Still, there is some subjectivity with regards to whether an answer should be deleted or not. Questionable answers can always be brought up on meta, and if an answer was unjustly deleted, any mod can undelete it.
Comments and chat
As has been said multiple times, comments are not the place to have discussions or debates! That's what the chat room is for, and other chat rooms may be created for specific topics. Comments are meant to be constructive. Ask for clarification, suggest support, point out that the answer doesn't actually answer the question, or point out an error. Now, pointing out an error does not mean that you say some claim is wrong, especially not if you disagree with it. Rather, pointing out an error is pointing out a factual error, like asking if someone meant to cite Exodus or Deuteronomy. If you disagree with it on a subjective basis, don't downvote or comment to that effect.
Again, don't debate in comments! Take it to chat!
Comments are meant to be disposable and are routinely deleted for being obsolete or unconstructive.
As a final word, I want to stress that this site is truly run by the community. Moderators are exception-handlers. That said, I am part of the community too, and this is what I think should be done.