I'll take your specific questions in turn
Should I continue to craft and cite this article?
If you take due note of the conflict of interest guidelines it shouldn't present an insurmountable a problem.
Can I cite news articles which we possess the paper copy of?
Yes please do cite newspaper articles - they are exactly the type of reliable sources we need to establish notability. The Cite news template is probably the easiest way to reference a newspaper article - you basically copy the "form" into the article at the point you want to insert the reference then fill in as many of it's fields as you can. Unpublished documents (from the company's own files) cannot be used as they are not verifiable.
Do you feel Muhlenberg Greene Architects has as much, if not more, merit in being a Wikipedia article as Muhlenberg Brothers?
I have no opinion on this - each article stands or falls based on its own merits.
Should I author this article, despite working for the current form of the organization?
Same answer as for the first question. 
To obviate the confusion between the two companies you can add a hatnote to the top of each article explaining the relationship between them.