The earliest uses I find of the phrase are in the 1950s, in the works of Alan Frank Guttmacher, a distinguished ob/gyn physician and author of several books on sexuality and reproductive health addressed to the general public.
There are scattered uses in Google Books through the 60s and 70s, but since the 80s the phrase has been widely used, not only in popular magazines and newspapers but also in academic books and peer-reviewed journals in obstetrics, nursing, psychotherapy and social work.
Pregnant does not necessarily mean physiologically gravid. In English it was first used in the sense “compelling” (a pregnant argument) as early as the last quarter of the 14th century, and MED records only a single use of the “literal” sense (ca. 1425) against ten uses in figurative or derived senses such as “imaginative, discerning, highly significant” and “compelling, weighty”. The physiological sense is undoubtedly primary now, but none of the other senses has entirely disappeared—consider “pregnant pause”, which choster cites, “pregnant wit”, “pregnant with hope”.
In light of those uses, it seems a bit churlish for grammarians to deny a mother (and her medical supporters) the right to implicate the father in the burden of pregnancy as well as its inception.
At any rate, “pregnant couple” is widely employed, and presumably just as widely accepted. You must decide for yourself whether it is acceptable to you.