To me, it seems very arbitrary to use different acronyms for the same dating system. As a non-Christian I don't understand why it's an issue that the naming comes from Christian tradition.
Is there any data on its usage and the preference of historians?
Is there a difference in the preference of historians and the preference of editors/publishers?
I had a quick look at a couple dozen books in my library, and less than one third of them used CE/BCE. (Note this is a non-random sample with mostly political and military history.)
When studying history from an academic perspective, its usually desirable to remain as culturally neutral as possible so as not to obscure the facts with a point-of-view. Its a subtle thing, but taking some efforts to step back and have a more objective point of view can be helpful when examining controversial issues.
Personally I use BCE and AD because I'm 'lazy'. BCE/AD don't require dots (usually) while B.C. and C.E. do. Obviously that isn't universal, sometimes you are required to use dots for all abbreviations. On the other hand, as long as you use one of the common abbreviations, which one matters less than the consistency of the use. If you start mixing BC/BCE or AD/CE in a text, that's not acceptable.