"Prima facie" evidence means your evidence prevails if it's not rebutted. Also, the question at issue is one of the company's "intent", not the mere fact of non-use. Rebuttal evidence could be made by showing the registration was unintentionally abandoned, and that there was an ongoing intent to keep using it. It is possible for companies to justify a period of non-use. (I wouldn't want to be in their shoes having to do it, but it can be done.) Also, note that the Lanham Act section you've cited relates to registration under the Lanham Act, although courts can look to that for guidance in determining abandonment of common law marks.
This isn't to say you can't use the mark or that the former owner is out there ready to bite you. I'm just saying you should proceed cautiously and realize that if you haven't checked beyond the PTO list of marks, there could be someone, whether the former owner of the registration or someone else, out there using the mark or a confusingly similar one on competing goods. A full common law search of any proposed new mark is always a good idea, in my opinion.