UTF-8 is always a tricky issue. It is not difficult to detect if there are some non-ASCII chars in the BibTeX output, but the question is what to do with them. Deleting is simply no option, since it will change the meaning, for example, of the title. For the case of Greek letters it will not be too difficult to implement a mapping to the LaTeX equivalent, but I am afraid that there will be some cases where a mapping cannot be established. For those cases we could provide a comment in the BibTeX output saying that there is a UTF-8 char that will cause trouble.
Fixed by now, Paperpile automatically converts β to $\beta$.
@ARTICLE{Gullo2014-fa, title = "Multi-electrode array study of neuronal cultures expressing nicotinic $\beta$2-V287L subunits, linked to autosomal dominant nocturnal frontal lobe epilepsy. An in vitro model of spontaneous epilepsy",